[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/11541273/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/11555654/transformed.cor.cli.txt"

nPatients in clinical file=250, in cluster file=295, common to both=238
[1]  80 238
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               74               164 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               74               164 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              117               121 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              117               121 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               52               186 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               52               186 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               31               207 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               31               207 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               61               177 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               61               177 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              147                91 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              147                91 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               229 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               229 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               226 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               226 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               87               151 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               87               151 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               36               202 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               36               202 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               44               194 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               44               194 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               29               209 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               29               209 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               32               206 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               32               206 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               30               208 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               30               208 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               199 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               199 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               66               172 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               66               172 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               39               199 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               39               199 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               37               201 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               37               201 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                218 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                218 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                226 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                226 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                230 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                230 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                231 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                231 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                44                194 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                44                194 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                41                197 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                41                197 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                217 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                217 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                35                203 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                35                203 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                45                193 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                45                193 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                33                205 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                33                205 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                29                209 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                29                209 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                220 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                220 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                36                202 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                36                202 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                34                204 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                34                204 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                217 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                217 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                39                199 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                39                199 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                58                180 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                58                180 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                81                157 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                81                157 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                94                144 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                94                144 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                207 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                207 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                26                212 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                26                212 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               33               205 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               33               205 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               11               227 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               11               227 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               229 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               229 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               223 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               223 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27               211 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27               211 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               171 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               171 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               228 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               228 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              104               134 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              104               134 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               76               162 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               76               162 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               17               221 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               17               221 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               45               193 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               45               193 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               39               199 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               39               199 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               59               179 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               59               179 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               21               217 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               21               217 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               32               206 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               32               206 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               68               170 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               68               170 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               218 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               218 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               45               193 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               45               193 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               39               199 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               39               199 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                50                188 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                50                188 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                59                179 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                59                179 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                81                157 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                81                157 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                93                145 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                93                145 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                29                209 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                29                209 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                10                228 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                10                228 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                66                172 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                66                172 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                28                210 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                28                210 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                34                204 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                34                204 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                29                209 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                29                209 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                35                203 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                35                203 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                78                160 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                78                160 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                208 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                208 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                45                193 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                45                193 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                59                179 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                59                179 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                49                189 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                49                189 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                25                213 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                25                213 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                219 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                219 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                230 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                230 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                196 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                196 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                180 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                180 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               44               194 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               44               194 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                    
 [2] "VITALSTATUS"                                     
 [3] "DAYSTODEATH"                                     
 [4] "DAYSTOLASTFOLLOWUP"                              
 [5] "PRIMARYSITEOFDISEASE"                            
 [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_TOTAL_DOSE"                            
[30] "RADIATION_THERAPY_TYPE"                          
[31] "RADIATION_THERAPY_STATUS"                        
[32] "RADIATION_THERAPY_SITE"                          
[33] "RADIATION_ADJUVANT_UNITS"                        
[34] "PREGNANCIES_COUNT_TOTAL"                         
[35] "PREGNANCIES_COUNT_STILLBIRTH"                    
[36] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[38] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[39] "PREGNANCIES_COUNT_ECTOPIC"                       
[40] "PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[41] "POS_LYMPH_NODE_LOCATION"                         
[42] "MENOPAUSE_STATUS"                                
[43] "LYMPHOVASCULAR_INVOLVEMENT"                      
[44] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[45] "LYMPH_NODES_EXAMINED"                            
[46] "KERATINIZATION_SQUAMOUS_CELL"                    
[47] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[48] "HYSTERECTOMY_TYPE"                               
[49] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[50] "HEIGHT_CM_AT_DIAGNOSIS"                          
[51] "FEDPET_OR_CT_RESULTS"                            
[52] "CORPUS_INVOLVEMENT"                              
[53] "CHEMO_CONCURRENT_TYPE"                           
[54] "CERVIX_SUV_RESULTS"                              
[55] "CAUSE_OF_DEATH"                                  
[56] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[57] "AGE_AT_DIAGNOSIS"                                
[58] "STAGE_EVENT.CLINICAL_STAGE"                      

Input Data has 58 rows and 238 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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
          NA           NA          109         1345         2226         2234 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
        2526         2383           NA         1169           25         1582 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
         548           NA          621         5564         4694           NA 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
          NA           NA          619         4482           NA         2602 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
        1846           NA           NA           NA           83         1551 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
          NA          254         2305         3039           NA           NA 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
         186          636          136           34         1791         1544 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1367         1218         2669         1791           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        3589         3609          699          512           NA          533 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
          NA           23          376           53           40           25 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
          19          397           36          441           41           41 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
         441           55          385          390            8          453 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
          45          423          457          456          455          413 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
         410           11          383         1398          799          202 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
          46           NA           NA           13           18           18 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
          44            4          489            2          123            1 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
          11           36           NA          721           68            3 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
           2            3            3           NA            1          619 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
         241          211          447          602          186          144 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
          37          725           28           66           20           31 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
          44           48           45           25          107           41 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
          40           60           34          274          773          217 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
          NA          632          454          287         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-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
        1106          834           NA          747          652          623 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
         474          306          156          204           NA         5957 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AV TCGA-LP-A4AW TCGA-LP-A4AX 
         922          243          343           NA           27            2 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
           9           25            6          422            1          165 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
         904            2          132          167           90          474 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
         406          485          103          491          534          428 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
         483          179          190          316          596          118 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
          NA           NA           NA         1864           NA         1050 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
         883          615          428           NA         1628           NA 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
        1400          708           NA         1507           NA           NA 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
          NA           NA          707         1365         1295         1280 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
        1333         1197         1185          549 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=164,	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=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	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=33,	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=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=70,	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=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASMHISTOLOGICGRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'RADIATION_TOTAL_DOSE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 31:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'RADIATION_THERAPY_SITE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 33:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 40:'PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 41:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 42:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 45:'LYMPH_NODES_EXAMINED':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 47:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 48:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 49:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 50:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 51:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 52:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 53:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 54:'CERVIX_SUV_RESULTS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 55:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 56:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 57:'AGE_AT_DIAGNOSIS':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 58:'STAGE_EVENT.CLINICAL_STAGE':	nDistinctValues=16,	numeric=FALSE,	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_TOTAL_DOSE"                            
[20] "RADIATION_THERAPY_TYPE"                          
[21] "RADIATION_THERAPY_STATUS"                        
[22] "RADIATION_THERAPY_SITE"                          
[23] "RADIATION_ADJUVANT_UNITS"                        
[24] "PREGNANCIES_COUNT_TOTAL"                         
[25] "PREGNANCIES_COUNT_STILLBIRTH"                    
[26] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[27] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[28] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[29] "PREGNANCIES_COUNT_ECTOPIC"                       
[30] "POS_LYMPH_NODE_LOCATION"                         
[31] "MENOPAUSE_STATUS"                                
[32] "LYMPHOVASCULAR_INVOLVEMENT"                      
[33] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[34] "LYMPH_NODES_EXAMINED"                            
[35] "KERATINIZATION_SQUAMOUS_CELL"                    
[36] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[37] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[38] "HEIGHT_CM_AT_DIAGNOSIS"                          
[39] "CORPUS_INVOLVEMENT"                              
[40] "CERVIX_SUV_RESULTS"                              
[41] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[42] "AGE_AT_DIAGNOSIS"                                
[43] "STAGE_EVENT.CLINICAL_STAGE"                      
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 238 columns, 1 survival variables, and 43 non-survival variables.
AGE, nv=58, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
121  50   9   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  121    50    11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
121  50   9   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  121    50    11 
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=33, 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=70, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=7, binary=FALSE, numeric=FALSE
NEOPLASMHISTOLOGICGRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=19, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=33, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=25, binary=FALSE, numeric=TRUE
RADIATION_TOTAL_DOSE, nv=34, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_SITE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_ADJUVANT_UNITS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=14, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=6, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=11, binary=FALSE, numeric=TRUE
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=48, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=33, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=13, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=15, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=58, binary=FALSE, numeric=TRUE
STAGE_EVENT.CLINICAL_STAGE, nv=16, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    56  16
  1P GAIN WILD-TYPE 127  34
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               72               161 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16                34 
$`1P GAIN MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        36.56       177.04        82.85        31.40        46.32 
TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A2LZ TCGA-C5-A3HF 
       38.99         0.46         2.43        20.91       100.14        17.85 
TCGA-C5-A7CJ TCGA-C5-A7X8 TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KL TCGA-DR-A0ZL 
      101.82         2.73        23.51        27.52        44.94        87.75 
TCGA-DS-A0VL TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A439 
        2.66         0.76         1.74         0.62         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2GZ 
        1.81        13.91        15.02        14.96         0.36        12.59 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
        1.51         0.59         0.59        16.08         1.18         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A3NI 
        0.10         0.07         0.03         6.94        19.79         1.45 
TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-IR-A3LL 
        1.58         1.35        20.78        14.93       117.40        36.36 
TCGA-JW-A5VK TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A5U2 
       20.48         6.71       195.85        30.31         7.99         0.30 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-R2-A69V 
        0.82        13.87         0.07         2.96        13.35        19.59 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QF 
       93.99        12.16        20.22        19.96        11.51        49.55 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       31.27        16.64        42.58        42.08        39.35        38.96 

$`1P GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ 
       57.04        23.67        11.44        68.84        18.74       144.16 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 
      173.29         5.46        19.86        67.46        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       57.73        53.16        35.61        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-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK 
       52.01        18.02        20.42       182.93       154.32       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       75.78        99.91         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       58.88        50.76        40.04        58.88        36.76       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        17.52         8.28 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       12.36         1.32         0.82        13.05         1.18        14.50 
TCGA-EA-A410 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-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       14.99        13.58        13.48        45.96        26.27         6.64 
TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.43         1.45         0.13         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.36        23.70         0.10         0.10        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         6.12         4.73         1.22        23.84         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-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       21.67         9.44       147.39       137.16        66.81        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        26.56        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3PZ TCGA-LP-A4AU 
       21.44        15.58        10.06         5.13        21.11        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.89         0.07         0.20         0.03         5.42        29.72 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        4.34         5.49        15.58        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        3.88        11.67        61.28        10.03        34.52        29.03 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH 
       14.07        53.52        32.15        46.03        23.28        39.78 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A958 TCGA-WL-A834 
        4.73        23.24        44.88        43.82        18.05 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           195.85            182.93 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           14.945            16.140 
[1] "0.0 - 195.8 (14.9)" "0.0 - 182.9 (16.1)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                T1 T2 T3+T4
  1P GAIN MUTATED   32 20     4
  1P GAIN WILD-TYPE 89 30     7
D1V3, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                 32                89
  T2                 20                30
  T3+T4               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   32 15
  1P GAIN WILD-TYPE 79 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     32   15
  1P GAIN WILD-TYPE   79   32
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              32                79
  1              15                32
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1P GAIN MUTATED   31  2 27
  1P GAIN WILD-TYPE 60  6 66
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              31                60
  M1               2                 6
  MX              27                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED               0                               68
  1P GAIN WILD-TYPE             5                              129
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1P GAIN MUTATED                                               1
  1P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1P GAIN MUTATED                                     3
  1P GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1P GAIN MUTATED                                           0
  1P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1P GAIN MUTATED                                              2
  1P GAIN WILD-TYPE                                            4
D1V6, multiclass
                                               clus
vv                                              1P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           68
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              1P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            129
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  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"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8  66
  1P GAIN WILD-TYPE  22 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8   66
  1P GAIN WILD-TYPE   22  142
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                8                22
  YES              66               142
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     9
  1P GAIN WILD-TYPE                                7     9
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED                           9
  1P GAIN WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0    48
  1P GAIN WILD-TYPE                                         1   121
D1V10, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   9                 9
  BLACK OR AFRICAN AMERICAN                               9                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  48               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"
D1V11, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     3  47
  1P GAIN WILD-TYPE  13 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3   47
  1P GAIN WILD-TYPE   13  102
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              47               102
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   17  9
  1P GAIN WILD-TYPE 54 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     17    9
  1P GAIN WILD-TYPE   54   16
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  TUMOR FREE              17                54
  WITH TUMOR               9                16
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  1P GAIN MUTATED       10      1       1      4       3            49       6
  1P GAIN WILD-TYPE     13      4       0      6       4           129       8
D1V14, multiclass
               clus
vv              1P GAIN MUTATED 1P GAIN WILD-TYPE
  BRAZIL                     10                13
  CANADA                      1                 4
  NIGERIA                     1                 0
  RUSSIA                      4                 6
  UKRAINE                     3                 4
  UNITED STATES              49               129
  VIETNAM                     6                 8
[1] 7 2
[1] 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    4 34 35  0  1
  1P GAIN WILD-TYPE 13 72 62  1 13
D1V15, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  G1               4                13
  G2              34                72
  G3              35                62
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V16, continuous
D1V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1P GAIN MUTATED                                             6
  1P GAIN WILD-TYPE                                          25
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1P GAIN MUTATED               17                  37
  1P GAIN WILD-TYPE             35                  75
D1V18, multiclass
                                                 clus
vv                                                1P 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                                               17
  LIFELONG NON-SMOKER                                          37
                                                 clus
vv                                                1P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 35
  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"
D1V19, continuous
D1V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  1P GAIN MUTATED             7       22             1        2
  1P GAIN WILD-TYPE          12       53            11       10
D1V21, multiclass
               clus
vv              1P GAIN MUTATED 1P GAIN WILD-TYPE
  COMBINATION                 7                12
  EXTERNAL                   22                53
  EXTERNAL BEAM               1                11
  INTERNAL                    2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V22, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    6  1
  1P GAIN WILD-TYPE 19  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6    1
  1P GAIN WILD-TYPE   19    2
                         clus
vv                        1P GAIN MUTATED 1P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  6                19
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  1P GAIN MUTATED                    0                0                   9
  1P GAIN WILD-TYPE                  2                2                  19
                   vv
clus                REGIONAL SITE
  1P GAIN MUTATED               7
  1P GAIN WILD-TYPE             9
D1V23, multiclass
                     clus
vv                    1P GAIN MUTATED 1P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               9                19
  REGIONAL SITE                     7                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V24, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   14  1
  1P GAIN WILD-TYPE 20  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     14    1
  1P GAIN WILD-TYPE   20    2
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  CGY              14                20
  GY                1                 2
[1] 2 2
[1] FALSE
D1V25, continuous
D1V26, continuous
D1V27, continuous
D1V28, continuous
D1V29, continuous
D1V30, 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                       7
  1P GAIN WILD-TYPE                                   6                      22
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1P GAIN MUTATED                         0                       2
  1P GAIN WILD-TYPE                       1                       5
D1V31, multiclass
                                     clus
vv                                    1P GAIN MUTATED 1P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           7                22
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 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)
  1P GAIN MUTATED                                               0
  1P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  1P GAIN MUTATED                                                5
  1P GAIN WILD-TYPE                                             11
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1P GAIN MUTATED                                                                                  30
  1P GAIN WILD-TYPE                                                                                38
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1P GAIN MUTATED                                                                                             28
  1P GAIN WILD-TYPE                                                                                           77
D1V32, multiclass
                                                                                              clus
vv                                                                                             1P 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)                         30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              28
                                                                                              clus
vv                                                                                             1P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V33, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   19 22
  1P GAIN WILD-TYPE 49 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     19   22
  1P GAIN WILD-TYPE   49   48
         clus
vv        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ABSENT               19                49
  PRESENT              22                48
[1] 2 2
[1] FALSE
D1V34, continuous
D1V35, continuous
D1V36, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   14 29
  1P GAIN WILD-TYPE 29 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     14   29
  1P GAIN WILD-TYPE   29   65
                                          clus
vv                                         1P GAIN MUTATED 1P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  14                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              29                65
[1] 2 2
[1] FALSE
D1V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1P GAIN MUTATED              3           8         21
  1P GAIN WILD-TYPE            7          41         36
D1V38, multiclass
              clus
vv             1P GAIN MUTATED 1P GAIN WILD-TYPE
  CURRENT USER               3                 7
  FORMER USER                8                41
  NEVER USED                21                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"
D1V39, continuous
D1V40, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   25  6
  1P GAIN WILD-TYPE 64 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     25    6
  1P GAIN WILD-TYPE   64   10
         clus
vv        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ABSENT               25                64
  PRESENT               6                10
[1] 2 2
[1] FALSE
D1V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  1P GAIN MUTATED     1    0   7   19    5  1   5    4    1   9  1   3  0   0
  1P GAIN WILD-TYPE   0    1  23   46   19  3   3    3    8  13  0   5  2   1
                   vv
clus                TX
  1P GAIN MUTATED    5
  1P GAIN WILD-TYPE  9
D1V42, multiclass
      clus
vv     1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1A                1                 0
  T1A1               0                 1
  T1B                7                23
  T1B1              19                46
  T1B2               5                19
  T2                 1                 3
  T2A                5                 3
  T2A1               4                 3
  T2A2               1                 8
  T2B                9                13
  T3                 1                 0
  T3B                3                 5
  T4                 0                 2
  TIS                0                 1
  TX                 5                 9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  1P GAIN MUTATED         0        1         0         0       11        20
  1P GAIN WILD-TYPE       4        1         1         1       20        49
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  1P GAIN MUTATED           6        1         2          3          2
  1P GAIN WILD-TYPE        26        2         4          2          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  1P GAIN MUTATED           9         1         14         1         1
  1P GAIN WILD-TYPE        18         0         20         2         6
D1V44, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                11                20
  STAGE IB1               20                49
  STAGE IB2                6                26
  STAGE II                 1                 2
  STAGE IIA                2                 4
  STAGE IIA1               3                 2
  STAGE IIA2               2                 5
  STAGE IIB                9                18
  STAGE III                1                 0
  STAGE IIIB              14                20
  STAGE IVA                1                 2
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   87 26
  1Q GAIN WILD-TYPE 96 24
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              113               120 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26                24 
$`1Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       49.48        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH 
       82.85         5.46        31.40        46.32        53.16        38.99 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY 
        0.46         2.43        20.91         3.58        44.22        78.35 
TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UI 
      100.14        17.85       101.82       134.33        15.48        94.95 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR 
        2.73        50.99        45.83         8.35        23.51        27.52 
TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ 
        1.12        44.94        87.75        58.88         2.66        22.98 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT 
       17.52         8.28         0.76         1.74         1.32         0.62 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        1.35        14.50         1.81        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
        1.51         0.59         0.59        16.08         1.18         2.24 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.10         0.03         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A40J 
        6.12         4.73        23.84         2.17         1.45         1.35 
TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LC TCGA-IR-A3LL 
        7.13        20.78        14.93         9.44       117.40        36.36 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       21.44        20.48         5.13         6.71       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MY-A5BE 
        7.99        11.28         0.30         0.82        13.87         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
        2.96        13.35        15.95         5.88         6.25        19.59 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL 
       93.99        12.16        10.03        20.22        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X 
       32.15        46.03        11.51        49.55        31.27        16.64 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        39.35        38.96        18.05 

$`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       154.32        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XJ TCGA-C5-A8XK 
       85.55        60.69         9.34        13.61        75.78        99.91 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM 
        6.12        20.91         4.47        58.88        50.76        40.04 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QT 
       36.76       117.99       118.65        16.83        16.18        12.36 
TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S 
        0.82        13.05         1.18        14.50         1.35        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2H1 TCGA-EK-A2IP 
       12.82         0.26        14.89         1.48        26.27         6.64 
TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.43         1.45         0.13         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-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       25.41        21.67       147.39       137.16        66.81        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        26.56        27.42         3.29        24.56 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU 
       15.58        10.06        21.11         0.89         0.07         0.20 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
        0.03         5.42        29.72         4.34         5.49        15.58 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73S 
        3.39        16.14        17.56        14.07        15.88        10.39 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI 
        3.88        11.67        61.28        34.52        29.03        14.07 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A958 
       23.28        39.78         4.73        23.24        44.88        43.82 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           195.85            182.93 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            15.02             16.16 
[1] "0.0 - 195.8 (15.0)" "0.0 - 182.9 (16.2)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                T1 T2 T3+T4
  1Q GAIN MUTATED   51 31     6
  1Q GAIN WILD-TYPE 70 19     5
D2V3, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                 51                70
  T2                 31                19
  T3+T4               6                 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"
D2V4, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   53 22
  1Q GAIN WILD-TYPE 58 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     53   22
  1Q GAIN WILD-TYPE   58   25
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              53                58
  1              22                25
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   46  5 45
  1Q GAIN WILD-TYPE 45  3 48
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              46                45
  M1               5                 3
  MX              45                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
  1Q GAIN MUTATED               3                              101
  1Q GAIN WILD-TYPE             2                               96
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1Q GAIN MUTATED                                               2
  1Q GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1Q GAIN MUTATED                                     9
  1Q GAIN WILD-TYPE                                  13
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1Q GAIN MUTATED                                           0
  1Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1Q GAIN MUTATED                                              2
  1Q GAIN WILD-TYPE                                            4
D2V6, multiclass
                                               clus
vv                                              1Q GAIN MUTATED
  ADENOSQUAMOUS                                               3
  CERVICAL SQUAMOUS CELL CARCINOMA                          101
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              1Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                             96
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  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"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    17 100
  1Q GAIN WILD-TYPE  13 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17  100
  1Q GAIN WILD-TYPE   13  108
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               17                13
  YES             100               108
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1    13
  1Q GAIN WILD-TYPE                                7     5
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED                          14
  1Q GAIN WILD-TYPE                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0    80
  1Q GAIN WILD-TYPE                                         1    89
D2V10, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                  13                 5
  BLACK OR AFRICAN AMERICAN                              14                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  80                89
[1] 5 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    5 71
  1Q GAIN WILD-TYPE 11 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   71
  1Q GAIN WILD-TYPE   11   78
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                11
  NOT HISPANIC OR LATINO              71                78
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   34 13
  1Q GAIN WILD-TYPE 37 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     34   13
  1Q GAIN WILD-TYPE   37   12
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  TUMOR FREE              34                37
  WITH TUMOR              13                12
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  1Q GAIN MUTATED       14      2       1      5       3            82      10
  1Q GAIN WILD-TYPE      9      3       0      5       4            96       4
D2V14, multiclass
               clus
vv              1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  BRAZIL                     14                 9
  CANADA                      2                 3
  NIGERIA                     1                 0
  RUSSIA                      5                 5
  UKRAINE                     3                 4
  UNITED STATES              82                96
  VIETNAM                    10                 4
[1] 7 2
[1] 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    6 52 53  0  5
  1Q GAIN WILD-TYPE 11 54 44  1  9
D2V15, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  G1               6                11
  G2              52                54
  G3              53                44
  G4               0                 1
  GX               5                 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"
D2V16, continuous
D2V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1Q GAIN MUTATED                                            13
  1Q GAIN WILD-TYPE                                          18
                   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                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1Q GAIN MUTATED               28                  57
  1Q GAIN WILD-TYPE             24                  55
D2V18, multiclass
                                                 clus
vv                                                1Q 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                                               28
  LIFELONG NON-SMOKER                                          57
                                                 clus
vv                                                1Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 24
  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"
D2V19, continuous
D2V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  1Q GAIN MUTATED            13       38             4        3
  1Q GAIN WILD-TYPE           6       37             8        9
D2V21, multiclass
               clus
vv              1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COMBINATION                13                 6
  EXTERNAL                   38                37
  EXTERNAL BEAM               4                 8
  INTERNAL                    3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V22, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   14  2
  1Q GAIN WILD-TYPE 11  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14    2
  1Q GAIN WILD-TYPE   11    1
                         clus
vv                        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                 14                11
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  1Q GAIN MUTATED                    1                0                  13
  1Q GAIN WILD-TYPE                  1                2                  15
                   vv
clus                REGIONAL SITE
  1Q GAIN MUTATED               9
  1Q GAIN WILD-TYPE             7
D2V23, multiclass
                     clus
vv                    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  DISTANT RECURRENCE                1                 1
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD              13                15
  REGIONAL SITE                     9                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V24, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   18  2
  1Q GAIN WILD-TYPE 16  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18    2
  1Q GAIN WILD-TYPE   16    1
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CGY              18                16
  GY                2                 1
[1] 2 2
[1] FALSE
D2V25, continuous
D2V26, continuous
D2V27, continuous
D2V28, continuous
D2V29, continuous
D2V30, 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                      15
  1Q GAIN WILD-TYPE                                   6                      14
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1Q GAIN MUTATED                         0                       3
  1Q GAIN WILD-TYPE                       1                       4
D2V31, multiclass
                                     clus
vv                                    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                          15                14
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 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)
  1Q GAIN MUTATED                                               0
  1Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  1Q GAIN MUTATED                                                8
  1Q GAIN WILD-TYPE                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1Q GAIN MUTATED                                                                                  38
  1Q GAIN WILD-TYPE                                                                                30
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1Q GAIN MUTATED                                                                                             51
  1Q GAIN WILD-TYPE                                                                                           54
D2V32, multiclass
                                                                                              clus
vv                                                                                             1Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              51
                                                                                              clus
vv                                                                                             1Q 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)                           30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V33, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   28 35
  1Q GAIN WILD-TYPE 40 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     28   35
  1Q GAIN WILD-TYPE   40   35
         clus
vv        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ABSENT               28                40
  PRESENT              35                35
[1] 2 2
[1] FALSE
D2V34, continuous
D2V35, continuous
D2V36, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   19 47
  1Q GAIN WILD-TYPE 24 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     19   47
  1Q GAIN WILD-TYPE   24   47
                                          clus
vv                                         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  19                24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              47                47
[1] 2 2
[1] FALSE
D2V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1Q GAIN MUTATED              4          21         28
  1Q GAIN WILD-TYPE            6          28         29
D2V38, multiclass
              clus
vv             1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CURRENT USER               4                 6
  FORMER USER               21                28
  NEVER USED                28                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"
D2V39, continuous
D2V40, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   37  7
  1Q GAIN WILD-TYPE 52  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     37    7
  1Q GAIN WILD-TYPE   52    9
         clus
vv        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ABSENT               37                52
  PRESENT               7                 9
[1] 2 2
[1] FALSE
D2V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  1Q GAIN MUTATED     1    0  10   30   10  2   7    6    2  14  1   5  0   0
  1Q GAIN WILD-TYPE   0    1  20   35   14  2   1    1    7   8  0   3  2   1
                   vv
clus                TX
  1Q GAIN MUTATED   10
  1Q GAIN WILD-TYPE  4
D2V42, multiclass
      clus
vv     1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1A                1                 0
  T1A1               0                 1
  T1B               10                20
  T1B1              30                35
  T1B2              10                14
  T2                 2                 2
  T2A                7                 1
  T2A1               6                 1
  T2A2               2                 7
  T2B               14                 8
  T3                 1                 0
  T3B                5                 3
  T4                 0                 2
  TIS                0                 1
  TX                10                 4
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  1Q GAIN MUTATED         2        1         0         0       14        31
  1Q GAIN WILD-TYPE       2        1         1         1       17        38
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  1Q GAIN MUTATED          12        2         3          4          3
  1Q GAIN WILD-TYPE        20        1         3          1          4
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  1Q GAIN MUTATED          15         1         20         2         3
  1Q GAIN WILD-TYPE        12         0         14         1         4
D2V44, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                14                17
  STAGE IB1               31                38
  STAGE IB2               12                20
  STAGE II                 2                 1
  STAGE IIA                3                 3
  STAGE IIA1               4                 1
  STAGE IIA2               3                 4
  STAGE IIB               15                12
  STAGE III                1                 0
  STAGE IIIB              20                14
  STAGE IVA                2                 1
  STAGE IVB                3                 4
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    40  11
  2P GAIN WILD-TYPE 143  39
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               51               182 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11                39 
$`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-C5-A7XC TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ 
       50.99        23.51         1.12        58.88        44.94        22.98 
TCGA-DS-A7WH TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A5ZF 
       17.52         1.35        14.50         1.81        14.89        14.96 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM 
       12.59        26.27         0.59        16.08         1.18         2.24 
TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-FU-A23L TCGA-FU-A40J TCGA-IR-A3LC TCGA-JW-A5VJ 
        0.10         7.92        23.84         1.35       117.40        21.44 
TCGA-JX-A5QV TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73S TCGA-UC-A7PD 
        7.99         5.49        13.35        15.95        10.39        11.67 
TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 
       93.99        14.07        49.55        16.64         4.73        44.88 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35       100.14        38.43        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       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A8XH 
       20.35       147.35        17.19        85.55        94.95        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        75.78        99.91        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        4.47        50.76        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI 
        2.66       117.99       118.65        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-A44S TCGA-EA-A4BA 
       13.05         1.18        14.50         1.35        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        15.02        14.99        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       13.48         0.36        45.96         6.64         1.51         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         1.45         0.13         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
        0.36        23.70         0.10         0.07         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
       20.35         6.94        14.70        19.79         6.12         4.73 
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-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       14.93         9.44       147.39       137.16        66.81        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85        30.31        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        13.87         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        15.58         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         5.88         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59         3.88        12.16        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       29.03        20.22        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A954 
       23.28        11.51        39.78        31.27        23.24        42.58 
TCGA-VS-A957 TCGA-VS-A958 
       42.08        43.82 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           117.40            195.85 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            14.96             16.01 
[1] "0.1 - 117.4 (15.0)" "0.0 - 195.8 (16.0)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                T1 T2 T3+T4
  2P GAIN MUTATED   23 11     2
  2P GAIN WILD-TYPE 98 39     9
D3V3, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                 23                98
  T2                 11                39
  T3+T4               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   22  8
  2P GAIN WILD-TYPE 89 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     22    8
  2P GAIN WILD-TYPE   89   39
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              22                89
  1               8                39
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2P GAIN MUTATED   20  1 17
  2P GAIN WILD-TYPE 71  7 76
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              20                71
  M1               1                 7
  MX              17                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED               2                               41
  2P GAIN WILD-TYPE             3                              156
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2P GAIN MUTATED                                               0
  2P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2P GAIN MUTATED                                     6
  2P GAIN WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2P GAIN MUTATED                                           1
  2P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2P GAIN MUTATED                                              2
  2P GAIN WILD-TYPE                                            4
D3V6, multiclass
                                               clus
vv                                              2P GAIN MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           41
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              2P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 3
  CERVICAL SQUAMOUS CELL CARCINOMA                            156
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     5  47
  2P GAIN WILD-TYPE  25 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5   47
  2P GAIN WILD-TYPE   25  161
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                5                25
  YES              47               161
[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                                6    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED                           4
  2P GAIN WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           1    36
  2P GAIN WILD-TYPE                                         0   133
D3V10, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 6
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               4                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  36               133
[1] 5 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     3  27
  2P GAIN WILD-TYPE  13 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   27
  2P GAIN WILD-TYPE   13  122
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              27               122
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   14  7
  2P GAIN WILD-TYPE 57 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     14    7
  2P GAIN WILD-TYPE   57   18
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  TUMOR FREE              14                57
  WITH TUMOR               7                18
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  2P GAIN MUTATED        7      3       0      2       1            37       2
  2P GAIN WILD-TYPE     16      2       1      8       6           141      12
D3V14, multiclass
               clus
vv              2P GAIN MUTATED 2P GAIN WILD-TYPE
  BRAZIL                      7                16
  CANADA                      3                 2
  NIGERIA                     0                 1
  RUSSIA                      2                 8
  UKRAINE                     1                 6
  UNITED STATES              37               141
  VIETNAM                     2                12
[1] 7 2
[1] 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    3 20 26  0  3
  2P GAIN WILD-TYPE 14 86 71  1 11
D3V15, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  G1               3                14
  G2              20                86
  G3              26                71
  G4               0                 1
  GX               3                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"
D3V16, continuous
D3V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2P GAIN MUTATED                                             7
  2P GAIN WILD-TYPE                                          24
                   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                                                 1
  2P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2P GAIN MUTATED               11                  22
  2P GAIN WILD-TYPE             41                  90
D3V18, multiclass
                                                 clus
vv                                                2P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               11
  LIFELONG NON-SMOKER                                          22
                                                 clus
vv                                                2P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 41
  LIFELONG NON-SMOKER                                            90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V19, continuous
D3V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  2P GAIN MUTATED             3       18             2        5
  2P GAIN WILD-TYPE          16       57            10        7
D3V21, multiclass
               clus
vv              2P GAIN MUTATED 2P GAIN WILD-TYPE
  COMBINATION                 3                16
  EXTERNAL                   18                57
  EXTERNAL BEAM               2                10
  INTERNAL                    5                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V22, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    5  0
  2P GAIN WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5    0
  2P GAIN WILD-TYPE   20    3
                         clus
vv                        2P GAIN MUTATED 2P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  2P GAIN MUTATED                    0                0                   9
  2P GAIN WILD-TYPE                  2                2                  19
                   vv
clus                REGIONAL SITE
  2P GAIN MUTATED               4
  2P GAIN WILD-TYPE            12
D3V23, multiclass
                     clus
vv                    2P GAIN MUTATED 2P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               9                19
  REGIONAL SITE                     4                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V24, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    9  1
  2P GAIN WILD-TYPE 25  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      9    1
  2P GAIN WILD-TYPE   25    2
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  CGY               9                25
  GY                1                 2
[1] 2 2
[1] FALSE
D3V25, continuous
D3V26, continuous
D3V27, continuous
D3V28, continuous
D3V29, continuous
D3V30, 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                       7
  2P GAIN WILD-TYPE                                   5                      22
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2P GAIN MUTATED                         0                       1
  2P GAIN WILD-TYPE                       1                       6
D3V31, multiclass
                                     clus
vv                                    2P GAIN MUTATED 2P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           7                22
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  2P GAIN MUTATED                                               0
  2P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  2P GAIN MUTATED                                                3
  2P GAIN WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2P GAIN MUTATED                                                                                  14
  2P GAIN WILD-TYPE                                                                                54
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2P GAIN MUTATED                                                                                             22
  2P GAIN WILD-TYPE                                                                                           83
D3V32, multiclass
                                                                                              clus
vv                                                                                             2P 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)                         14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              22
                                                                                              clus
vv                                                                                             2P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V33, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   12 16
  2P GAIN WILD-TYPE 56 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12   16
  2P GAIN WILD-TYPE   56   54
         clus
vv        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ABSENT               12                56
  PRESENT              16                54
[1] 2 2
[1] FALSE
D3V34, continuous
D3V35, continuous
D3V36, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    8 17
  2P GAIN WILD-TYPE 35 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8   17
  2P GAIN WILD-TYPE   35   77
                                          clus
vv                                         2P GAIN MUTATED 2P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              17                77
[1] 2 2
[1] FALSE
D3V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2P GAIN MUTATED              4          13         10
  2P GAIN WILD-TYPE            6          36         47
D3V38, multiclass
              clus
vv             2P GAIN MUTATED 2P GAIN WILD-TYPE
  CURRENT USER               4                 6
  FORMER USER               13                36
  NEVER USED                10                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"
D3V39, continuous
D3V40, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   15  6
  2P GAIN WILD-TYPE 74 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15    6
  2P GAIN WILD-TYPE   74   10
         clus
vv        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ABSENT               15                74
  PRESENT               6                10
[1] 2 2
[1] FALSE
D3V41, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                11 
       TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  2P GAIN MUTATED     0    0   5   17    1  0   2    3    1   5  0   2  0   1
  2P GAIN WILD-TYPE   1    1  25   48   23  4   6    4    8  17  1   6  2   0
                   vv
clus                TX
  2P GAIN MUTATED    3
  2P GAIN WILD-TYPE 11
D3V42, multiclass
      clus
vv     2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                5                25
  T1B1              17                48
  T1B2               1                23
  T2                 0                 4
  T2A                2                 6
  T2A1               3                 4
  T2A2               1                 8
  T2B                5                17
  T3                 0                 1
  T3B                2                 6
  T4                 0                 2
  TIS                1                 0
  TX                 3                11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  2P GAIN MUTATED         0        0         0         0        3        20
  2P GAIN WILD-TYPE       4        2         1         1       28        49
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  2P GAIN MUTATED           4        0         2          2          1
  2P GAIN WILD-TYPE        28        3         4          3          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  2P GAIN MUTATED           9         0          7         0         1
  2P GAIN WILD-TYPE        18         1         27         3         6
D3V44, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                28
  STAGE IB1               20                49
  STAGE IB2                4                28
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               2                 3
  STAGE IIA2               1                 6
  STAGE IIB                9                18
  STAGE III                0                 1
  STAGE IIIB               7                27
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    23   7
  2Q GAIN WILD-TYPE 160  43
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               30               203 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                43 
$`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-C5-A8YQ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A7WH 
        9.34         2.73        23.51         1.12        58.88        17.52 
TCGA-DS-A7WI TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2H1 
        8.28        14.50         1.81        14.96        12.59        26.27 
TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-FU-A40J TCGA-MY-A913 TCGA-Q1-A73S 
        0.59         1.18         2.24         1.35         5.49        10.39 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A959 TCGA-WL-A834 
       11.67        93.99        14.07        49.55        39.35        18.05 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-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       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       85.55        94.95        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       75.78        99.91        27.52         6.12        20.91         4.47 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        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-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-A44S 
       13.05         1.18        14.50         1.35         1.35        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        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.99        13.58        13.48         0.36        45.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        1.51         0.43         0.59         1.45         0.13        16.08 
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-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-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       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        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        5.13         6.71        21.11       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89         0.07         0.30         0.82         0.20 
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        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
       17.56        14.07        15.88         5.88         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        3.88        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       20.22        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       11.51        39.78        31.27        16.64         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 
       44.88        42.58        42.08        43.82        38.96 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            93.99            195.85 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           14.285            16.080 
[1] "0.5 - 94.0 (14.3)"  "0.0 - 195.8 (16.1)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                 T1  T2 T3+T4
  2Q GAIN MUTATED    14   5     1
  2Q GAIN WILD-TYPE 107  45    10
D4V3, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                 14               107
  T2                  5                45
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    10   8
  2Q GAIN WILD-TYPE 101  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     10    8
  2Q GAIN WILD-TYPE  101   39
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              10               101
  1               8                39
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2Q GAIN MUTATED   12  1  8
  2Q GAIN WILD-TYPE 79  7 85
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              12                79
  M1               1                 7
  MX               8                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED               2                               25
  2Q GAIN WILD-TYPE             3                              172
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2Q GAIN MUTATED                                               0
  2Q GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2Q GAIN MUTATED                                     3
  2Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2Q GAIN MUTATED                                           0
  2Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2Q GAIN MUTATED                                              1
  2Q GAIN WILD-TYPE                                            5
D4V6, multiclass
                                               clus
vv                                              2Q GAIN MUTATED
  ADENOSQUAMOUS                                               2
  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                1
                                               clus
vv                                              2Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 3
  CERVICAL SQUAMOUS CELL CARCINOMA                            172
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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  28
  2Q GAIN WILD-TYPE  27 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   28
  2Q GAIN WILD-TYPE   27  180
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                3                27
  YES              28               180
[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                                7    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED                           2
  2Q GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0    22
  2Q GAIN WILD-TYPE                                         1   147
D4V10, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               2                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  22               147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     1  18
  2Q GAIN WILD-TYPE  15 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   18
  2Q GAIN WILD-TYPE   15  131
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              18               131
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    6  5
  2Q GAIN WILD-TYPE 65 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      6    5
  2Q GAIN WILD-TYPE   65   20
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  TUMOR FREE               6                65
  WITH TUMOR               5                20
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  2Q GAIN MUTATED        3      2       0      0       1            23       2
  2Q GAIN WILD-TYPE     20      3       1     10       6           155      12
D4V14, multiclass
               clus
vv              2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  BRAZIL                      3                20
  CANADA                      2                 3
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     1                 6
  UNITED STATES              23               155
  VIETNAM                     2                12
[1] 7 2
[1] 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 15 14  0  2
  2Q GAIN WILD-TYPE 17 91 83  1 12
D4V15, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  G1               0                17
  G2              15                91
  G3              14                83
  G4               0                 1
  GX               2                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"
D4V16, continuous
D4V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2Q GAIN MUTATED                                             4
  2Q GAIN WILD-TYPE                                          27
                   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                                                 1
  2Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2Q GAIN MUTATED                6                  12
  2Q GAIN WILD-TYPE             46                 100
D4V18, multiclass
                                                 clus
vv                                                2Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                6
  LIFELONG NON-SMOKER                                          12
                                                 clus
vv                                                2Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 46
  LIFELONG NON-SMOKER                                           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"
D4V19, continuous
D4V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  2Q GAIN MUTATED             2       11             1        3
  2Q GAIN WILD-TYPE          17       64            11        9
D4V21, multiclass
               clus
vv              2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COMBINATION                 2                17
  EXTERNAL                   11                64
  EXTERNAL BEAM               1                11
  INTERNAL                    3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V22, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3  0
  2Q GAIN WILD-TYPE 22  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    0
  2Q GAIN WILD-TYPE   22    3
                         clus
vv                        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  3                22
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  2Q GAIN MUTATED                    0                0                   4
  2Q GAIN WILD-TYPE                  2                2                  24
                   vv
clus                REGIONAL SITE
  2Q GAIN MUTATED               3
  2Q GAIN WILD-TYPE            13
D4V23, multiclass
                     clus
vv                    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               4                24
  REGIONAL SITE                     3                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V24, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4  1
  2Q GAIN WILD-TYPE 30  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    1
  2Q GAIN WILD-TYPE   30    2
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CGY               4                30
  GY                1                 2
[1] 2 2
[1] FALSE
D4V25, continuous
D4V26, continuous
D4V27, continuous
D4V28, continuous
D4V29, continuous
D4V30, 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                       4
  2Q GAIN WILD-TYPE                                   5                      25
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2Q GAIN MUTATED                         0                       0
  2Q GAIN WILD-TYPE                       1                       7
D4V31, multiclass
                                     clus
vv                                    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           4                25
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             14
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2Q GAIN MUTATED                                                                                   6
  2Q GAIN WILD-TYPE                                                                                62
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2Q GAIN MUTATED                                                                                             15
  2Q GAIN WILD-TYPE                                                                                           90
D4V32, 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)              15
                                                                                              clus
vv                                                                                             2Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V33, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4 13
  2Q GAIN WILD-TYPE 64 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   13
  2Q GAIN WILD-TYPE   64   57
         clus
vv        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ABSENT                4                64
  PRESENT              13                57
[1] 2 2
[1] FALSE
D4V34, continuous
D4V35, continuous
D4V36, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4 12
  2Q GAIN WILD-TYPE 39 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   12
  2Q GAIN WILD-TYPE   39   82
                                          clus
vv                                         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   4                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              12                82
[1] 2 2
[1] FALSE
D4V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2Q GAIN MUTATED              1           7          5
  2Q GAIN WILD-TYPE            9          42         52
D4V38, multiclass
              clus
vv             2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                7                42
  NEVER USED                 5                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"
D4V39, continuous
D4V40, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    7  4
  2Q GAIN WILD-TYPE 82 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      7    4
  2Q GAIN WILD-TYPE   82   12
         clus
vv        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ABSENT                7                82
  PRESENT               4                12
[1] 2 2
[1] FALSE
D4V41, continuous
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  2Q GAIN MUTATED     0    0   3   10    1  0   1    2    1   1  0   1  0   1
  2Q GAIN WILD-TYPE   1    1  27   55   23  4   7    5    8  21  1   7  2   0
                   vv
clus                TX
  2Q GAIN MUTATED    1
  2Q GAIN WILD-TYPE 13
D4V42, multiclass
      clus
vv     2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                3                27
  T1B1              10                55
  T1B2               1                23
  T2                 0                 4
  T2A                1                 7
  T2A1               2                 5
  T2A2               1                 8
  T2B                1                21
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                1                 0
  TX                 1                13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  2Q GAIN MUTATED         0        0         0         0        3        11
  2Q GAIN WILD-TYPE       4        2         1         1       28        58
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  2Q GAIN MUTATED           2        0         1          1          1
  2Q GAIN WILD-TYPE        30        3         5          4          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  2Q GAIN MUTATED           5         0          6         0         0
  2Q GAIN WILD-TYPE        22         1         28         3         7
D4V44, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                28
  STAGE IB1               11                58
  STAGE IB2                2                30
  STAGE II                 0                 3
  STAGE IIA                1                 5
  STAGE IIA1               1                 4
  STAGE IIA2               1                 6
  STAGE IIB                5                22
  STAGE III                0                 1
  STAGE IIIB               6                28
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    41  18
  3P GAIN WILD-TYPE 142  32
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               59               174 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               18                32 
$`3P GAIN MUTATED`
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       46.32        30.21        35.01        53.16        38.99         0.46 
TCGA-C5-A1ML TCGA-C5-A2LT TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CJ 
       20.91        73.18         0.82        18.02        17.85       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-DG-A2KH 
      134.33        15.48         9.34        50.99         8.35         1.12 
TCGA-DG-A2KJ TCGA-DS-A0VL TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 
       58.88         2.66        17.52         8.28         0.76        14.50 
TCGA-EA-A50E TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R9 
        0.26        14.96        12.59         1.51         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RM TCGA-EX-A69L TCGA-FU-A3TX TCGA-GH-A9DA TCGA-HG-A2PA 
       16.08         2.24        19.79         1.48         9.01        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LA TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       21.67        20.78       137.16         5.13       195.85        30.31 
TCGA-LP-A4AU TCGA-LP-A7HU TCGA-MU-A8JM TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A73O 
       11.28         0.20         5.42         2.96        15.58        14.07 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       11.67        12.16        10.03        14.07        19.96        53.52 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A957 TCGA-VS-A959 
       23.28        49.55        31.27        42.08        39.35 

$`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-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-A1ME TCGA-C5-A1MI TCGA-C5-A1MK 
       19.86        67.46        31.40        57.73        35.61         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-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
      100.14        38.43        52.01        20.42       182.93       154.32 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       13.61         2.73        45.83        75.78        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL 
       27.52         6.12        20.91         4.47        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       40.04        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-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-A556 TCGA-EA-A5FO 
        1.35         1.81        12.66        12.82        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       13.91        15.02        14.99        13.58        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       45.96        26.27         6.64         0.43         0.59         1.45 
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-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-EX-A8YF TCGA-FU-A23K 
        7.92         6.94        14.70         6.12         4.73         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-A9SC TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
        1.12         7.13        14.93         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX 
       10.06         6.71        21.11         7.99         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
        0.30         0.82        13.87         0.03        29.72         0.07 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        4.34         5.49        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       17.56        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
        3.88        93.99        61.28        34.52        29.03        20.22 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y 
       32.15        46.03        11.51        39.78        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       23.24        44.88        42.58        43.82        38.96        18.05 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.13              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           195.85            182.93 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           15.580            15.915 
[1] "0.1 - 195.8 (15.6)" "0.0 - 182.9 (15.9)"
[1] "hr=" "1.8"
D5V2, continuous
                   vv
clus                T1 T2 T3+T4
  3P GAIN MUTATED   27 12     6
  3P GAIN WILD-TYPE 94 38     5
D5V3, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                 27                94
  T2                 12                38
  T3+T4               6                 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"
D5V4, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   28 10
  3P GAIN WILD-TYPE 83 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     28   10
  3P GAIN WILD-TYPE   83   37
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              28                83
  1              10                37
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED   22  3 22
  3P GAIN WILD-TYPE 69  5 71
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              22                69
  M1               3                 5
  MX              22                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED               1                               50
  3P GAIN WILD-TYPE             4                              147
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3P GAIN MUTATED                                               0
  3P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3P GAIN MUTATED                                     7
  3P GAIN WILD-TYPE                                  15
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3P GAIN MUTATED                                           1
  3P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3P GAIN MUTATED                                              2
  3P GAIN WILD-TYPE                                            4
D5V6, multiclass
                                               clus
vv                                              3P GAIN MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              3P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            147
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  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"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     9  52
  3P GAIN WILD-TYPE  21 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9   52
  3P GAIN WILD-TYPE   21  156
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                9                21
  YES              52               156
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     7
  3P GAIN WILD-TYPE                                7    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED                           7
  3P GAIN WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           0    38
  3P GAIN WILD-TYPE                                         1   131
D5V10, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   7                11
  BLACK OR AFRICAN AMERICAN                               7                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  38               131
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4  33
  3P GAIN WILD-TYPE  12 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   33
  3P GAIN WILD-TYPE   12  116
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                12
  NOT HISPANIC OR LATINO              33               116
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   15 10
  3P GAIN WILD-TYPE 56 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15   10
  3P GAIN WILD-TYPE   56   15
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  TUMOR FREE              15                56
  WITH TUMOR              10                15
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  3P GAIN MUTATED        9      2       1      1       0            43       5
  3P GAIN WILD-TYPE     14      3       0      9       7           135       9
D5V14, multiclass
               clus
vv              3P GAIN MUTATED 3P GAIN WILD-TYPE
  BRAZIL                      9                14
  CANADA                      2                 3
  NIGERIA                     1                 0
  RUSSIA                      1                 9
  UKRAINE                     0                 7
  UNITED STATES              43               135
  VIETNAM                     5                 9
[1] 7 2
[1] 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    1 27 27  0  6
  3P GAIN WILD-TYPE 16 79 70  1  8
D5V15, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  G1               1                16
  G2              27                79
  G3              27                70
  G4               0                 1
  GX               6                 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"
D5V16, continuous
D5V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3P GAIN MUTATED                                             9
  3P GAIN WILD-TYPE                                          22
                   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                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3P GAIN MUTATED               14                  27
  3P GAIN WILD-TYPE             38                  85
D5V18, multiclass
                                                 clus
vv                                                3P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               14
  LIFELONG NON-SMOKER                                          27
                                                 clus
vv                                                3P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 38
  LIFELONG NON-SMOKER                                            85
[1] 5 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
D5V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  3P GAIN MUTATED             4       21             5        2
  3P GAIN WILD-TYPE          15       54             7       10
D5V21, multiclass
               clus
vv              3P GAIN MUTATED 3P GAIN WILD-TYPE
  COMBINATION                 4                15
  EXTERNAL                   21                54
  EXTERNAL BEAM               5                 7
  INTERNAL                    2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V22, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    8  0
  3P GAIN WILD-TYPE 17  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      8    0
  3P GAIN WILD-TYPE   17    3
                         clus
vv                        3P GAIN MUTATED 3P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  8                17
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  3P GAIN MUTATED                    0                1                   5
  3P GAIN WILD-TYPE                  2                1                  23
                   vv
clus                REGIONAL SITE
  3P GAIN MUTATED               4
  3P GAIN WILD-TYPE            12
D5V23, multiclass
                     clus
vv                    3P GAIN MUTATED 3P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               5                23
  REGIONAL SITE                     4                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V24, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    7  1
  3P GAIN WILD-TYPE 27  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      7    1
  3P GAIN WILD-TYPE   27    2
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  CGY               7                27
  GY                1                 2
[1] 2 2
[1] FALSE
D5V25, continuous
D5V26, continuous
D5V27, continuous
D5V28, continuous
D5V29, continuous
D5V30, 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                      12
  3P GAIN WILD-TYPE                                   5                      17
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3P GAIN MUTATED                         1                       1
  3P GAIN WILD-TYPE                       0                       6
D5V31, multiclass
                                     clus
vv                                    3P GAIN MUTATED 3P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                          12                17
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  3P GAIN MUTATED                                               1
  3P GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  3P GAIN MUTATED                                                2
  3P GAIN WILD-TYPE                                             14
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3P GAIN MUTATED                                                                                  18
  3P GAIN WILD-TYPE                                                                                50
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3P GAIN MUTATED                                                                                             26
  3P GAIN WILD-TYPE                                                                                           79
D5V32, multiclass
                                                                                              clus
vv                                                                                             3P 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)                         18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              26
                                                                                              clus
vv                                                                                             3P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              14
  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)                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V33, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   15 14
  3P GAIN WILD-TYPE 53 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15   14
  3P GAIN WILD-TYPE   53   56
         clus
vv        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ABSENT               15                53
  PRESENT              14                56
[1] 2 2
[1] FALSE
D5V34, continuous
D5V35, continuous
D5V36, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   10 24
  3P GAIN WILD-TYPE 33 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     10   24
  3P GAIN WILD-TYPE   33   70
                                          clus
vv                                         3P GAIN MUTATED 3P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              24                70
[1] 2 2
[1] FALSE
D5V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3P GAIN MUTATED              2          11         15
  3P GAIN WILD-TYPE            8          38         42
D5V38, multiclass
              clus
vv             3P GAIN MUTATED 3P GAIN WILD-TYPE
  CURRENT USER               2                 8
  FORMER USER               11                38
  NEVER USED                15                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V39, continuous
D5V40, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   19  4
  3P GAIN WILD-TYPE 70 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     19    4
  3P GAIN WILD-TYPE   70   12
         clus
vv        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ABSENT               19                70
  PRESENT               4                12
[1] 2 2
[1] FALSE
D5V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  3P GAIN MUTATED     0    0   8   14    5  2   1    1    2   6  1   4  1   0
  3P GAIN WILD-TYPE   1    1  22   51   19  2   7    6    7  16  0   4  1   1
                   vv
clus                TX
  3P GAIN MUTATED    3
  3P GAIN WILD-TYPE 11
D5V42, multiclass
      clus
vv     3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                8                22
  T1B1              14                51
  T1B2               5                19
  T2                 2                 2
  T2A                1                 7
  T2A1               1                 6
  T2A2               2                 7
  T2B                6                16
  T3                 1                 0
  T3B                4                 4
  T4                 1                 1
  TIS                0                 1
  TX                 3                11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  3P GAIN MUTATED         0        0         0         0        5        18
  3P GAIN WILD-TYPE       4        2         1         1       26        51
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  3P GAIN MUTATED           9        1         2          1          3
  3P GAIN WILD-TYPE        23        2         4          4          4
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  3P GAIN MUTATED           8         1          9         2         1
  3P GAIN WILD-TYPE        19         0         25         1         6
D5V44, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 5                26
  STAGE IB1               18                51
  STAGE IB2                9                23
  STAGE II                 1                 2
  STAGE IIA                2                 4
  STAGE IIA1               1                 4
  STAGE IIA2               3                 4
  STAGE IIB                8                19
  STAGE III                1                 0
  STAGE IIIB               9                25
  STAGE IVA                2                 1
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   109  35
  3Q GAIN WILD-TYPE  74  15
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              144                89 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               35                15 
$`3Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        23.67        11.44        36.56       144.16       177.04 
TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       82.85        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       57.73        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.18        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CJ 
       78.35       100.14         0.82        18.02        17.85       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
      134.33        15.48        85.55        94.95         9.34         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       50.99         8.35        23.51         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        40.04        87.75        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
      118.65        22.98        16.83        17.52         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-A439 TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       14.50         0.26         1.48        13.91        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 
       14.96         0.36        12.59         1.51         0.59         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RL TCGA-EK-A2RM 
        0.13        16.08         0.07         4.04        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L 
        0.10         0.07        20.35         6.94        19.79        23.84 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV 
        1.45         1.48         0.82         3.52         1.35         1.97 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
      137.16       117.40        36.36        21.44        20.48        15.58 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        5.13         6.71       195.85        30.31         7.99        11.28 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A913 TCGA-PN-A8MA 
        0.30         0.20        13.87         5.42         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        13.35        15.95         3.39        17.56        14.07 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
        3.88        11.67        93.99        12.16        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       29.03        14.07        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        11.51        49.55        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       23.24        42.58        42.08        39.35        38.96        18.05 

$`3Q GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ 
       57.04        68.84        18.74       173.29         5.46        19.86 
TCGA-C5-A2LV TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       73.45        38.43        52.01        20.42       182.93       154.32 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A8XH 
       20.35       147.35        17.19        60.69        13.61        45.83 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       75.78        99.91        27.52         6.12        20.91         4.47 
TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       58.88        16.18         1.18        14.50         1.35         1.35 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A6QX TCGA-EA-A78R 
        1.81        12.66        12.82        14.89        13.58        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RD 
       45.96        26.27         6.64         0.43         1.45         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
        0.36         1.18         0.10         0.10         0.03         7.92 
TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         6.12         4.73         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A6W2 
        0.66         1.02         1.58         1.32         1.12         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
      147.39        66.81        96.95        78.71        81.96        26.56 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AW 
       27.42         3.29        24.56        10.06        21.11         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.07         0.82         0.03        29.72         0.07         4.34 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       16.14        15.88         5.88         6.25        10.39        19.59 
TCGA-UC-A7PI TCGA-VS-A8EH TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A958 
       61.28        20.22        39.78        44.88        43.82 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           195.85            182.93 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           16.735            14.500 
[1] "0.1 - 195.8 (16.7)" "0.0 - 182.9 (14.5)"
[1] "hr=" "1.3"
D6V2, continuous
                   vv
clus                T1 T2 T3+T4
  3Q GAIN MUTATED   71 33     9
  3Q GAIN WILD-TYPE 50 17     2
D6V3, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                 71                50
  T2                 33                17
  T3+T4               9                 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"
D6V4, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   62 35
  3Q GAIN WILD-TYPE 49 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     62   35
  3Q GAIN WILD-TYPE   49   12
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              62                49
  1              35                12
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED   60  4 57
  3Q GAIN WILD-TYPE 31  4 36
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              60                31
  M1               4                 4
  MX              57                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED               2                              129
  3Q GAIN WILD-TYPE             3                               68
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3Q GAIN MUTATED                                               2
  3Q GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3Q GAIN MUTATED                                    10
  3Q GAIN WILD-TYPE                                  12
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3Q GAIN MUTATED                                           1
  3Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3Q GAIN MUTATED                                              3
  3Q GAIN WILD-TYPE                                            3
D6V6, multiclass
                                               clus
vv                                              3Q GAIN MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                          129
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                        10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                3
                                               clus
vv                                              3Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 3
  CERVICAL SQUAMOUS CELL CARCINOMA                             68
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          12
  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"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    22 125
  3Q GAIN WILD-TYPE   8  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     22  125
  3Q GAIN WILD-TYPE    8   83
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               22                 8
  YES             125                83
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  4    12
  3Q GAIN WILD-TYPE                                4     6
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED                          17
  3Q GAIN WILD-TYPE                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           0    98
  3Q GAIN WILD-TYPE                                         1    71
D6V10, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        4                 4
  ASIAN                                                  12                 6
  BLACK OR AFRICAN AMERICAN                              17                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  98                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"
D6V11, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    9 89
  3Q GAIN WILD-TYPE  7 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      9   89
  3Q GAIN WILD-TYPE    7   60
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                 7
  NOT HISPANIC OR LATINO              89                60
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   45 19
  3Q GAIN WILD-TYPE 26  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     45   19
  3Q GAIN WILD-TYPE   26    6
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  TUMOR FREE              45                26
  WITH TUMOR              19                 6
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  3Q GAIN MUTATED       19      5       1      6       3           104       9
  3Q GAIN WILD-TYPE      4      0       0      4       4            74       5
D6V14, multiclass
               clus
vv              3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  BRAZIL                     19                 4
  CANADA                      5                 0
  NIGERIA                     1                 0
  RUSSIA                      6                 4
  UKRAINE                     3                 4
  UNITED STATES             104                74
  VIETNAM                     9                 5
[1] 7 2
[1] 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    9 67 60  0 11
  3Q GAIN WILD-TYPE  8 39 37  1  3
D6V15, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  G1               9                 8
  G2              67                39
  G3              60                37
  G4               0                 1
  GX              11                 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"
D6V16, continuous
D6V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3Q GAIN MUTATED                                            20
  3Q GAIN WILD-TYPE                                          11
                   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                                                 2
  3Q GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3Q GAIN MUTATED               35                  70
  3Q GAIN WILD-TYPE             17                  42
D6V18, multiclass
                                                 clus
vv                                                3Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               35
  LIFELONG NON-SMOKER                                          70
                                                 clus
vv                                                3Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 17
  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"
D6V19, continuous
D6V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  3Q GAIN MUTATED            14       48             9        7
  3Q GAIN WILD-TYPE           5       27             3        5
D6V21, multiclass
               clus
vv              3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COMBINATION                14                 5
  EXTERNAL                   48                27
  EXTERNAL BEAM               9                 3
  INTERNAL                    7                 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"
D6V22, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   18  2
  3Q GAIN WILD-TYPE  7  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     18    2
  3Q GAIN WILD-TYPE    7    1
                         clus
vv                        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                 18                 7
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  3Q GAIN MUTATED                    0                2                  17
  3Q GAIN WILD-TYPE                  2                0                  11
                   vv
clus                REGIONAL SITE
  3Q GAIN MUTATED              10
  3Q GAIN WILD-TYPE             6
D6V23, multiclass
                     clus
vv                    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  2                 0
  PRIMARY TUMOR FIELD              17                11
  REGIONAL SITE                    10                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V24, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   23  2
  3Q GAIN WILD-TYPE 11  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     23    2
  3Q GAIN WILD-TYPE   11    1
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CGY              23                11
  GY                2                 1
[1] 2 2
[1] FALSE
D6V25, continuous
D6V26, continuous
D6V27, continuous
D6V28, continuous
D6V29, continuous
D6V30, 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                      22
  3Q GAIN WILD-TYPE                                   2                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3Q GAIN MUTATED                         1                       5
  3Q GAIN WILD-TYPE                       0                       2
D6V31, multiclass
                                     clus
vv                                    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               4                 2
  OTHER LOCATION, SPECIFY                          22                 7
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           5                 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                                                8
  3Q GAIN WILD-TYPE                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3Q GAIN MUTATED                                                                                  47
  3Q GAIN WILD-TYPE                                                                                21
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3Q GAIN MUTATED                                                                                             64
  3Q GAIN WILD-TYPE                                                                                           41
D6V32, multiclass
                                                                                              clus
vv                                                                                             3Q GAIN MUTATED
  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)              64
                                                                                              clus
vv                                                                                             3Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           21
  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"
D6V33, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   38 45
  3Q GAIN WILD-TYPE 30 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     38   45
  3Q GAIN WILD-TYPE   30   25
         clus
vv        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ABSENT               38                30
  PRESENT              45                25
[1] 2 2
[1] FALSE
D6V34, continuous
D6V35, continuous
D6V36, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   27 57
  3Q GAIN WILD-TYPE 16 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     27   57
  3Q GAIN WILD-TYPE   16   37
                                          clus
vv                                         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  27                16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              57                37
[1] 2 2
[1] FALSE
D6V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3Q GAIN MUTATED              7          32         32
  3Q GAIN WILD-TYPE            3          17         25
D6V38, multiclass
              clus
vv             3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CURRENT USER               7                 3
  FORMER USER               32                17
  NEVER USED                32                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V39, continuous
D6V40, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   54 10
  3Q GAIN WILD-TYPE 35  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     54   10
  3Q GAIN WILD-TYPE   35    6
         clus
vv        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ABSENT               54                35
  PRESENT              10                 6
[1] 2 2
[1] FALSE
D6V41, continuous
[1] "Remove cluster labels:" "3Q GAIN WILD-TYPE"     
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                 1 
     TCGA-C5-A1MH      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" 
     TCGA-EK-A2RO      TCGA-GH-A9DA      TCGA-HM-A3JK      TCGA-JW-A852 
"3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" 
     TCGA-JX-A3Q8      TCGA-MU-A51Y      TCGA-MU-A8JM      TCGA-MY-A913 
"3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  3Q GAIN MUTATED     0    0  17   40   14  4   6    5    3  15  1   7  1   1
  3Q GAIN WILD-TYPE   1    1  13   25   10  0   2    2    6   7  0   1  1   0
                   vv
clus                TX
  3Q GAIN MUTATED    9
  3Q GAIN WILD-TYPE  5
D6V42, multiclass
      clus
vv     3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B               17                13
  T1B1              40                25
  T1B2              14                10
  T2                 4                 0
  T2A                6                 2
  T2A1               5                 2
  T2A2               3                 6
  T2B               15                 7
  T3                 1                 0
  T3B                7                 1
  T4                 1                 1
  TIS                1                 0
  TX                 9                 5
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  3Q GAIN MUTATED         2        0         0         0       19        43
  3Q GAIN WILD-TYPE       2        2         1         1       12        26
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  3Q GAIN MUTATED          16        3         4          4          4
  3Q GAIN WILD-TYPE        16        0         2          1          3
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  3Q GAIN MUTATED          19         1         23         3         2
  3Q GAIN WILD-TYPE         8         0         11         0         5
D6V44, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                19                12
  STAGE IB1               43                26
  STAGE IB2               16                16
  STAGE II                 3                 0
  STAGE IIA                4                 2
  STAGE IIA1               4                 1
  STAGE IIA2               4                 3
  STAGE IIB               19                 8
  STAGE III                1                 0
  STAGE IIIB              23                11
  STAGE IVA                3                 0
  STAGE IVB                2                 5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     6   2
  4P GAIN WILD-TYPE 177  48
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               225 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                48 
$`4P GAIN MUTATED`
TCGA-C5-A1MN TCGA-C5-A7X5 TCGA-C5-A8XI TCGA-FU-A23K TCGA-IR-A3LF TCGA-JX-A3Q8 
       40.93        13.61         8.35         1.22        96.95        30.31 
TCGA-LP-A5U3 TCGA-R2-A69V 
        0.82        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-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43         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       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ 
       94.95         9.34         2.73        50.99        45.83        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        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        17.52         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        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.99        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
       45.96        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         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-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-EX-A8YF TCGA-FU-A23L 
        6.94        14.70        19.79         6.12         4.73        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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        6.71        21.11       195.85         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.07         0.30         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       29.72         0.07         4.34         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       13.35        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       15.88         5.88         6.25        10.39         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       20.22        14.07        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       23.28        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.82              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            96.95            195.85 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            16.60             15.88 
[1] "0.8 - 97.0 (16.6)"  "0.0 - 195.8 (15.9)"
[1] "hr=" "1.2"
D7V2, continuous
                   vv
clus                 T1  T2 T3+T4
  4P GAIN MUTATED     6   0     0
  4P GAIN WILD-TYPE 115  50    11
D7V3, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  6               115
  T2                  0                50
  T3+T4               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     5   1
  4P GAIN WILD-TYPE 106  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    1
  4P GAIN WILD-TYPE  106   46
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               5               106
  1               1                46
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4P GAIN MUTATED    3  0  3
  4P GAIN WILD-TYPE 88  8 90
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               3                88
  M1               0                 8
  MX               3                90
[1] 3 2
[1] 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                                7
  4P GAIN WILD-TYPE             5                              190
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4P GAIN MUTATED                                               1
  4P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4P GAIN MUTATED                                     1
  4P GAIN WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4P GAIN MUTATED                                           0
  4P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4P GAIN MUTATED                                              0
  4P GAIN WILD-TYPE                                            6
D7V6, multiclass
                                               clus
vv                                              4P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            7
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              4P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            190
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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   8
  4P GAIN WILD-TYPE  29 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    8
  4P GAIN WILD-TYPE   29  200
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                29
  YES               8               200
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                71 
       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-A1ML        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HF        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-A7UI        TCGA-C5-A7X8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7XC        TCGA-C5-A8XH        TCGA-C5-A8YQ        TCGA-C5-A8YT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A8ZZ        TCGA-DG-A2KK        TCGA-DG-A2KL        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-GH-A9DA        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-AAVH        TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-Q1-A73Q        TCGA-Q1-A73S        TCGA-RA-A741 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PG        TCGA-VS-A8EH        TCGA-VS-A8QM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VS-A94Y        TCGA-VS-A94Z        TCGA-WL-A834 
"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     2
  4P GAIN WILD-TYPE                                8    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED                           2
  4P GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0     5
  4P GAIN WILD-TYPE                                         1   164
D7V10, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               2                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               164
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   5
  4P GAIN WILD-TYPE  16 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    5
  4P GAIN WILD-TYPE   16  144
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               5               144
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  0
  4P GAIN WILD-TYPE 69 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    0
  4P GAIN WILD-TYPE   69   25
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  TUMOR FREE               2                69
  WITH TUMOR               0                25
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  4P GAIN MUTATED        0      0       0      0       0             8       1
  4P GAIN WILD-TYPE     23      5       1     10       7           170      13
D7V14, multiclass
               clus
vv              4P GAIN MUTATED 4P GAIN WILD-TYPE
  BRAZIL                      0                23
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 7
  UNITED STATES               8               170
  VIETNAM                     1                13
[1] 7 2
[1] 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   6   0   0
  4P GAIN WILD-TYPE  17 103  91   1  14
D7V15, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  G1               0                17
  G2               3               103
  G3               6                91
  G4               0                 1
  GX               0                14
[1] 5 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 
                2                71 
       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-A1ML        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HF        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-A7UI        TCGA-C5-A7X8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7XC        TCGA-C5-A8XH        TCGA-C5-A8YQ        TCGA-C5-A8YT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A8ZZ        TCGA-DG-A2KK        TCGA-DG-A2KL        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-GH-A9DA        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-AAVH        TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-Q1-A73Q        TCGA-Q1-A73S        TCGA-RA-A741 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PG        TCGA-VS-A8EH        TCGA-VS-A8QM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VS-A94Y        TCGA-VS-A94Z        TCGA-WL-A834 
"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                                          31
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4P GAIN MUTATED                2                   5
  4P GAIN WILD-TYPE             50                 107
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                                                2
  LIFELONG NON-SMOKER                                           5
                                                 clus
vv                                                4P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 50
  LIFELONG NON-SMOKER                                           107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V19, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                66 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A2LS        TCGA-C5-A2LT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7X8        TCGA-C5-A8YQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A8YT        TCGA-C5-A8ZZ        TCGA-C5-A907        TCGA-DG-A2KK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-EA-A556        TCGA-EK-A2RA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-GH-A9DA        TCGA-HM-A4S6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-JW-AAVH        TCGA-JX-A3Q0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-Q1-A73Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VS-A8EH        TCGA-VS-A8QF        TCGA-VS-A8QM        TCGA-VS-A94Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VS-A94Z        TCGA-WL-A834 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  4P GAIN MUTATED             1        4             0        0
  4P GAIN WILD-TYPE          18       71            12       12
D7V21, multiclass
               clus
vv              4P GAIN MUTATED 4P GAIN WILD-TYPE
  COMBINATION                 1                18
  EXTERNAL                    4                71
  EXTERNAL BEAM               0                12
  INTERNAL                    0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V22, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  0
  4P GAIN WILD-TYPE 24  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    0
  4P GAIN WILD-TYPE   24    3
                         clus
vv                        4P GAIN MUTATED 4P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  1                24
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  4P GAIN MUTATED                    0                0                   3
  4P GAIN WILD-TYPE                  2                2                  25
                   vv
clus                REGIONAL SITE
  4P GAIN MUTATED               0
  4P GAIN WILD-TYPE            16
D7V23, multiclass
                     clus
vv                    4P GAIN MUTATED 4P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               3                25
  REGIONAL SITE                     0                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V24, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  1
  4P GAIN WILD-TYPE 33  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    1
  4P GAIN WILD-TYPE   33    2
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  CGY               1                33
  GY                1                 2
[1] 2 2
[1] FALSE
D7V25, continuous
D7V26, continuous
D7V27, continuous
D7V28, continuous
D7V29, continuous
D7V30, continuous
                   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                       1
  4P GAIN WILD-TYPE                                   6                      28
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4P GAIN MUTATED                         0                       0
  4P GAIN WILD-TYPE                       1                       7
D7V31, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                44 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        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-A1MJ        TCGA-C5-A1MP 
"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-A2M1        TCGA-C5-A3HE        TCGA-C5-A3HL        TCGA-C5-A7CJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7UC        TCGA-C5-A7X8        TCGA-C5-A7XC        TCGA-C5-A8XH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DG-A2KL        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-EA-A50E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EK-A2RN        TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-HM-A4S6        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-MU-A8JM        TCGA-UC-A7PD        TCGA-VS-A8QA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  4P GAIN MUTATED                                               0
  4P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4P GAIN MUTATED                                                1
  4P GAIN WILD-TYPE                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4P GAIN MUTATED                                                                                   2
  4P GAIN WILD-TYPE                                                                                66
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4P GAIN MUTATED                                                                                              4
  4P GAIN WILD-TYPE                                                                                          101
D7V32, multiclass
                                                                                              clus
vv                                                                                             4P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               4
                                                                                              clus
vv                                                                                             4P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           66
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V33, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    3  2
  4P GAIN WILD-TYPE 65 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3    2
  4P GAIN WILD-TYPE   65   68
         clus
vv        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ABSENT                3                65
  PRESENT               2                68
[1] 2 2
[1] FALSE
D7V34, continuous
D7V35, continuous
D7V36, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  4
  4P GAIN WILD-TYPE 41 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    4
  4P GAIN WILD-TYPE   41   90
                                          clus
vv                                         4P GAIN MUTATED 4P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   2                41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               4                90
[1] 2 2
[1] FALSE
D7V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4P GAIN MUTATED              0           2          2
  4P GAIN WILD-TYPE           10          47         55
D7V38, multiclass
              clus
vv             4P GAIN MUTATED 4P GAIN WILD-TYPE
  CURRENT USER               0                10
  FORMER USER                2                47
  NEVER USED                 2                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"
D7V39, continuous
D7V40, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    4  0
  4P GAIN WILD-TYPE 85 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE   85   16
         clus
vv        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ABSENT                4                85
  PRESENT               0                16
[1] 2 2
[1] FALSE
D7V41, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                11 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  4P GAIN MUTATED     1    0   1    3    1  0   0    0    0   0  0   0  0   0
  4P GAIN WILD-TYPE   0    1  29   62   23  4   8    7    9  22  1   8  2   1
                   vv
clus                TX
  4P GAIN MUTATED    0
  4P GAIN WILD-TYPE 14
D7V42, multiclass
      clus
vv     4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1A                1                 0
  T1A1               0                 1
  T1B                1                29
  T1B1               3                62
  T1B2               1                23
  T2                 0                 4
  T2A                0                 8
  T2A1               0                 7
  T2A2               0                 9
  T2B                0                22
  T3                 0                 1
  T3B                0                 8
  T4                 0                 2
  TIS                0                 1
  TX                 0                14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  4P GAIN MUTATED         0        1         0         0        1         2
  4P GAIN WILD-TYPE       4        1         1         1       30        67
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  4P GAIN MUTATED           1        0         0          0          0
  4P GAIN WILD-TYPE        31        3         6          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  4P GAIN MUTATED           0         0          3         0         1
  4P GAIN WILD-TYPE        27         1         31         3         6
D7V44, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 1                30
  STAGE IB1                2                67
  STAGE IB2                1                31
  STAGE II                 0                 3
  STAGE IIA                0                 6
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                0                27
  STAGE III                0                 1
  STAGE IIIB               3                31
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    10   1
  4Q GAIN WILD-TYPE 173  49
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               11               222 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                49 
$`4Q GAIN MUTATED`
TCGA-C5-A1MP TCGA-C5-A7XC TCGA-C5-A8XI TCGA-EK-A3GK TCGA-FU-A23K TCGA-IR-A3LF 
        3.58        50.99         8.35         0.10         1.22        96.95 
TCGA-JX-A3Q8 TCGA-LP-A5U3 TCGA-MY-A5BF TCGA-R2-A69V TCGA-VS-A8QC 
       30.31         0.82         4.34        19.59        11.51 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93        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       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ 
       94.95         9.34        13.61         2.73        45.83        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        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        17.52         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        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.99        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
       45.96        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         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-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A2QG 
       14.70        19.79         6.12         4.73        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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
        9.44       147.39       137.16        66.81       117.40        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85         7.99        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.30         0.20        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         5.49         2.96        15.58        13.35        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        3.39        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
        6.25        10.39         3.88        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       61.28        10.03        34.52        29.03        20.22        14.07 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF 
       19.96        53.52        32.15        46.03        23.28        49.55 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        16.64         4.73        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.10              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            96.95            195.85 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            8.350            16.015 
[1] "0.1 - 97.0 (8.3)"   "0.0 - 195.8 (16.0)"
[1] "hr=" "1.7"
D8V2, continuous
                   vv
clus                 T1  T2 T3+T4
  4Q GAIN MUTATED     9   1     0
  4Q GAIN WILD-TYPE 112  49    11
D8V3, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  9               112
  T2                  1                49
  T3+T4               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     8   2
  4Q GAIN WILD-TYPE 103  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      8    2
  4Q GAIN WILD-TYPE  103   45
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               8               103
  1               2                45
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4Q GAIN MUTATED    4  0  7
  4Q GAIN WILD-TYPE 87  8 86
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               4                87
  M1               0                 8
  MX               7                86
[1] 3 2
[1] 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                                9
  4Q GAIN WILD-TYPE             5                              188
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4Q GAIN MUTATED                                               1
  4Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4Q GAIN MUTATED                                     2
  4Q GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4Q GAIN MUTATED                                           0
  4Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4Q GAIN MUTATED                                              0
  4Q GAIN WILD-TYPE                                            6
D8V6, multiclass
                                               clus
vv                                              4Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            9
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              4Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            188
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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  12
  4Q GAIN WILD-TYPE  30 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   12
  4Q GAIN WILD-TYPE   30  196
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                30
  YES              12               196
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                71 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"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-A1ML        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-A2LZ        TCGA-C5-A2M2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7X8        TCGA-C5-A8XH        TCGA-C5-A8YQ        TCGA-C5-A8YT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A8ZZ        TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DR-A0ZM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5 
"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-A3TQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GH-A9DA        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-AAVH        TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-Q1-A73Q        TCGA-Q1-A73S        TCGA-RA-A741 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PG        TCGA-VS-A8EH        TCGA-VS-A8QM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VS-A94Y        TCGA-VS-A94Z        TCGA-WL-A834 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     2
  4Q GAIN WILD-TYPE                                8    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED                           2
  4Q GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0     8
  4Q GAIN WILD-TYPE                                         1   161
D8V10, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               2                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               161
[1] 5 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   7
  4Q GAIN WILD-TYPE  16 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    7
  4Q GAIN WILD-TYPE   16  142
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               7               142
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    2  0
  4Q GAIN WILD-TYPE 69 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    0
  4Q GAIN WILD-TYPE   69   25
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  TUMOR FREE               2                69
  WITH TUMOR               0                25
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  4Q GAIN MUTATED        1      0       0      0       0            10       1
  4Q GAIN WILD-TYPE     22      5       1     10       7           168      13
D8V14, multiclass
               clus
vv              4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  BRAZIL                      1                22
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 7
  UNITED STATES              10               168
  VIETNAM                     1                13
[1] 7 2
[1] 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   4   7   0   0
  4Q GAIN WILD-TYPE  16 102  90   1  14
D8V15, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  G1               1                16
  G2               4               102
  G3               7                90
  G4               0                 1
  GX               0                14
[1] 5 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
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                71 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"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-A1ML        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-A2LZ        TCGA-C5-A2M2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7X8        TCGA-C5-A8XH        TCGA-C5-A8YQ        TCGA-C5-A8YT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A8ZZ        TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DR-A0ZM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5 
"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-A3TQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GH-A9DA        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-AAVH        TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-Q1-A73Q        TCGA-Q1-A73S        TCGA-RA-A741 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PG        TCGA-VS-A8EH        TCGA-VS-A8QM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VS-A94Y        TCGA-VS-A94Z        TCGA-WL-A834 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4Q GAIN MUTATED                                             0
  4Q GAIN WILD-TYPE                                          31
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4Q GAIN MUTATED                3                   7
  4Q GAIN WILD-TYPE             49                 105
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                                                3
  LIFELONG NON-SMOKER                                           7
                                                 clus
vv                                                4Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 49
  LIFELONG NON-SMOKER                                           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"
D8V19, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                66 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        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-A2LZ        TCGA-C5-A2M2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        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-A7X8        TCGA-C5-A8YQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A8YT        TCGA-C5-A8ZZ        TCGA-C5-A907        TCGA-DG-A2KK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-EA-A556        TCGA-EK-A2RA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-GH-A9DA        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-A3LB        TCGA-IR-A3LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-JW-AAVH        TCGA-JX-A3Q0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-Q1-A73Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VS-A8EH        TCGA-VS-A8QF        TCGA-VS-A8QM        TCGA-VS-A94Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VS-A94Z        TCGA-WL-A834 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  4Q GAIN MUTATED             0        4             0        0
  4Q GAIN WILD-TYPE          19       71            12       12
D8V21, multiclass
               clus
vv              4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COMBINATION                 0                19
  EXTERNAL                    4                71
  EXTERNAL BEAM               0                12
  INTERNAL                    0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V22, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  0
  4Q GAIN WILD-TYPE 25  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    0
  4Q GAIN WILD-TYPE   25    3
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  4Q GAIN MUTATED                    0                0                   2
  4Q GAIN WILD-TYPE                  2                2                  26
                   vv
clus                REGIONAL SITE
  4Q GAIN MUTATED               1
  4Q GAIN WILD-TYPE            15
D8V23, multiclass
                     clus
vv                    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               2                26
  REGIONAL SITE                     1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V24, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    2  1
  4Q GAIN WILD-TYPE 32  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    1
  4Q GAIN WILD-TYPE   32    2
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CGY               2                32
  GY                1                 2
[1] 2 2
[1] FALSE
D8V25, continuous
D8V26, continuous
D8V27, continuous
D8V28, continuous
D8V29, continuous
D8V30, continuous
                   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                       3
  4Q GAIN WILD-TYPE                                   6                      26
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4Q GAIN MUTATED                         0                       0
  4Q GAIN WILD-TYPE                       1                       7
D8V31, multiclass
                                     clus
vv                                    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           3                26
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  4Q GAIN MUTATED                                               0
  4Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4Q GAIN MUTATED                                                2
  4Q GAIN WILD-TYPE                                             14
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4Q GAIN MUTATED                                                                                   3
  4Q GAIN WILD-TYPE                                                                                65
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4Q GAIN MUTATED                                                                                              4
  4Q GAIN WILD-TYPE                                                                                          101
D8V32, multiclass
                                                                                              clus
vv                                                                                             4Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               4
                                                                                              clus
vv                                                                                             4Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V33, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3  5
  4Q GAIN WILD-TYPE 65 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    5
  4Q GAIN WILD-TYPE   65   65
         clus
vv        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ABSENT                3                65
  PRESENT               5                65
[1] 2 2
[1] FALSE
D8V34, continuous
D8V35, continuous
D8V36, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  4
  4Q GAIN WILD-TYPE 43 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    4
  4Q GAIN WILD-TYPE   43   90
                                          clus
vv                                         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   0                43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               4                90
[1] 2 2
[1] FALSE
D8V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4Q GAIN MUTATED              1           1          2
  4Q GAIN WILD-TYPE            9          48         55
D8V38, multiclass
              clus
vv             4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                1                48
  NEVER USED                 2                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"
D8V39, continuous
D8V40, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    5  0
  4Q GAIN WILD-TYPE 84 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    0
  4Q GAIN WILD-TYPE   84   16
         clus
vv        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ABSENT                5                84
  PRESENT               0                16
[1] 2 2
[1] FALSE
D8V41, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                11 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  4Q GAIN MUTATED     1    0   2    4    2  0   0    0    1   0  0   0  0   0
  4Q GAIN WILD-TYPE   0    1  28   61   22  4   8    7    8  22  1   8  2   1
                   vv
clus                TX
  4Q GAIN MUTATED    1
  4Q GAIN WILD-TYPE 13
D8V42, multiclass
      clus
vv     4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1A                1                 0
  T1A1               0                 1
  T1B                2                28
  T1B1               4                61
  T1B2               2                22
  T2                 0                 4
  T2A                0                 8
  T2A1               0                 7
  T2A2               1                 8
  T2B                0                22
  T3                 0                 1
  T3B                0                 8
  T4                 0                 2
  TIS                0                 1
  TX                 1                13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  4Q GAIN MUTATED         0        1         0         0        1         4
  4Q GAIN WILD-TYPE       4        1         1         1       30        65
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  4Q GAIN MUTATED           2        0         0          0          1
  4Q GAIN WILD-TYPE        30        3         6          5          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  4Q GAIN MUTATED           0         0          2         1         0
  4Q GAIN WILD-TYPE        27         1         32         2         7
D8V44, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 1                30
  STAGE IB1                4                65
  STAGE IB2                2                30
  STAGE II                 0                 3
  STAGE IIA                0                 6
  STAGE IIA1               0                 5
  STAGE IIA2               1                 6
  STAGE IIB                0                27
  STAGE III                0                 1
  STAGE IIIB               2                32
  STAGE IVA                1                 2
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    66  17
  5P GAIN WILD-TYPE 117  33
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               83               150 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               17                33 
$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ 
       57.73        20.91        40.93         3.58        73.18       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       38.43        52.01        18.02        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       85.55        60.69         9.34         2.73        50.99        45.83 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       75.78        99.91        27.52         4.47         1.12        58.88 
TCGA-DG-A2KL TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3Y4 TCGA-EA-A439 
       44.94        22.98         0.76         1.32        14.50        14.50 
TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
        1.81        13.91        14.96         1.51         0.43         0.59 
TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
       16.08         1.18         0.10         0.10         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A5XV 
        6.94        19.79         4.73        23.84         1.45         1.97 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL 
        9.01        25.41        21.67        78.71        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A5QV TCGA-MY-A5BE 
       27.42        24.56         5.13         6.71         7.99         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-UC-A7PG TCGA-UC-A7PI 
        2.96        13.35        15.95         3.39        12.16        61.28 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94X 
       14.07        19.96        53.52        11.51        49.55        16.64 
TCGA-VS-A94Y TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
        4.73        43.82        39.35        38.96        18.05 

$`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       154.32       101.82       134.33        17.19        94.95 
TCGA-C5-A7X5 TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KK 
       13.61         8.35        23.51         6.12        20.91        50.76 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        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        17.52         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-EA-A97N TCGA-EK-A2GZ 
       15.02        14.99        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       45.96        26.27         6.64         0.59         1.45         0.13 
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-A2RO TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K 
        0.07         0.10         7.92        14.70         6.12         1.22 
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-A770 TCGA-HG-A9SC 
        0.82         3.52         1.35         1.32         1.12         7.13 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
      117.40        96.95        81.96         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
       15.58        10.06        21.11       195.85        30.31        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
        0.03         5.42        29.72         4.34         5.49        15.58 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         5.88         6.25 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB 
       10.39        19.59         3.88        11.67        93.99        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       34.52        29.03        20.22        32.15        46.03        23.28 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       39.78        31.27        23.24        44.88        42.58        42.08 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           147.35            195.85 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            19.79             14.91 
[1] "0.0 - 147.3 (19.8)" "0.0 - 195.8 (14.9)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                T1 T2 T3+T4
  5P GAIN MUTATED   33 23     3
  5P GAIN WILD-TYPE 88 27     8
D9V3, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                 33                88
  T2                 23                27
  T3+T4               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   35 13
  5P GAIN WILD-TYPE 76 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     35   13
  5P GAIN WILD-TYPE   76   34
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              35                76
  1              13                34
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED   32  1 30
  5P GAIN WILD-TYPE 59  7 63
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              32                59
  M1               1                 7
  MX              30                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
  5P GAIN MUTATED               1                               79
  5P GAIN WILD-TYPE             4                              118
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5P GAIN MUTATED                                               1
  5P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5P GAIN MUTATED                                     4
  5P GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5P GAIN MUTATED                                           1
  5P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5P GAIN MUTATED                                              1
  5P GAIN WILD-TYPE                                            5
D9V6, multiclass
                                               clus
vv                                              5P GAIN MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           79
  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                                              5P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 4
  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                  5
[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     9  78
  5P GAIN WILD-TYPE  21 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9   78
  5P GAIN WILD-TYPE   21  130
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                9                21
  YES              78               130
[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                                6    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED                          10
  5P GAIN WILD-TYPE                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0    65
  5P GAIN WILD-TYPE                                         1   104
D9V10, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 6
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                              10                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  65               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"
D9V11, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7  49
  5P GAIN WILD-TYPE   9 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   49
  5P GAIN WILD-TYPE    9  100
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 9
  NOT HISPANIC OR LATINO              49               100
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   26  9
  5P GAIN WILD-TYPE 45 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     26    9
  5P GAIN WILD-TYPE   45   16
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  TUMOR FREE              26                45
  WITH TUMOR               9                16
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  5P GAIN MUTATED       10      3       1      2       3            65       3
  5P GAIN WILD-TYPE     13      2       0      8       4           113      11
D9V14, multiclass
               clus
vv              5P GAIN MUTATED 5P GAIN WILD-TYPE
  BRAZIL                     10                13
  CANADA                      3                 2
  NIGERIA                     1                 0
  RUSSIA                      2                 8
  UKRAINE                     3                 4
  UNITED STATES              65               113
  VIETNAM                     3                11
[1] 7 2
[1] 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    4 34 41  1  4
  5P GAIN WILD-TYPE 13 72 56  0 10
D9V15, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  G1               4                13
  G2              34                72
  G3              41                56
  G4               1                 0
  GX               4                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"
D9V16, continuous
D9V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5P GAIN MUTATED                                            13
  5P GAIN WILD-TYPE                                          18
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5P GAIN MUTATED               21                  38
  5P GAIN WILD-TYPE             31                  74
D9V18, multiclass
                                                 clus
vv                                                5P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               21
  LIFELONG NON-SMOKER                                          38
                                                 clus
vv                                                5P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 31
  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"
D9V19, continuous
D9V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  5P GAIN MUTATED             5       36             3        6
  5P GAIN WILD-TYPE          14       39             9        6
D9V21, multiclass
               clus
vv              5P GAIN MUTATED 5P GAIN WILD-TYPE
  COMBINATION                 5                14
  EXTERNAL                   36                39
  EXTERNAL BEAM               3                 9
  INTERNAL                    6                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V22, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    9  0
  5P GAIN WILD-TYPE 16  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9    0
  5P GAIN WILD-TYPE   16    3
                         clus
vv                        5P GAIN MUTATED 5P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  5P GAIN MUTATED                    0                1                  18
  5P GAIN WILD-TYPE                  2                1                  10
                   vv
clus                REGIONAL SITE
  5P GAIN MUTATED               8
  5P GAIN WILD-TYPE             8
D9V23, multiclass
                     clus
vv                    5P GAIN MUTATED 5P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD              18                10
  REGIONAL SITE                     8                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V24, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   19  1
  5P GAIN WILD-TYPE 15  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     19    1
  5P GAIN WILD-TYPE   15    2
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  CGY              19                15
  GY                1                 2
[1] 2 2
[1] FALSE
D9V25, continuous
D9V26, continuous
D9V27, continuous
D9V28, continuous
D9V29, continuous
D9V30, 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                      11
  5P GAIN WILD-TYPE                                   4                      18
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5P GAIN MUTATED                         0                       2
  5P GAIN WILD-TYPE                       1                       5
D9V31, multiclass
                                     clus
vv                                    5P GAIN MUTATED 5P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 4
  OTHER LOCATION, SPECIFY                          11                18
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 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)
  5P GAIN MUTATED                                               0
  5P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5P GAIN MUTATED                                                3
  5P GAIN WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5P GAIN MUTATED                                                                                  23
  5P GAIN WILD-TYPE                                                                                45
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5P GAIN MUTATED                                                                                             36
  5P GAIN WILD-TYPE                                                                                           69
D9V32, multiclass
                                                                                              clus
vv                                                                                             5P 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)                         23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              36
                                                                                              clus
vv                                                                                             5P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           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"
D9V33, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   21 19
  5P GAIN WILD-TYPE 47 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     21   19
  5P GAIN WILD-TYPE   47   51
         clus
vv        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ABSENT               21                47
  PRESENT              19                51
[1] 2 2
[1] FALSE
D9V34, continuous
D9V35, continuous
D9V36, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   12 36
  5P GAIN WILD-TYPE 31 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     12   36
  5P GAIN WILD-TYPE   31   58
                                          clus
vv                                         5P GAIN MUTATED 5P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  12                31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              36                58
[1] 2 2
[1] FALSE
D9V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5P GAIN MUTATED              4          17         15
  5P GAIN WILD-TYPE            6          32         42
D9V38, multiclass
              clus
vv             5P GAIN MUTATED 5P GAIN WILD-TYPE
  CURRENT USER               4                 6
  FORMER USER               17                32
  NEVER USED                15                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V39, continuous
D9V40, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   23  5
  5P GAIN WILD-TYPE 66 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     23    5
  5P GAIN WILD-TYPE   66   11
         clus
vv        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ABSENT               23                66
  PRESENT               5                11
[1] 2 2
[1] FALSE
D9V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  5P GAIN MUTATED     0    0   8   18    7  0   4    5    1  13  0   3  0   0
  5P GAIN WILD-TYPE   1    1  22   47   17  4   4    2    8   9  1   5  2   1
                   vv
clus                TX
  5P GAIN MUTATED    6
  5P GAIN WILD-TYPE  8
D9V42, multiclass
      clus
vv     5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                8                22
  T1B1              18                47
  T1B2               7                17
  T2                 0                 4
  T2A                4                 4
  T2A1               5                 2
  T2A2               1                 8
  T2B               13                 9
  T3                 0                 1
  T3B                3                 5
  T4                 0                 2
  TIS                0                 1
  TX                 6                 8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  5P GAIN MUTATED         1        0         0         0        7        23
  5P GAIN WILD-TYPE       3        2         1         1       24        46
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  5P GAIN MUTATED          10        1         3          4          1
  5P GAIN WILD-TYPE        22        2         3          1          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  5P GAIN MUTATED          17         0         14         1         0
  5P GAIN WILD-TYPE        10         1         20         2         7
D9V44, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 7                24
  STAGE IB1               23                46
  STAGE IB2               10                22
  STAGE II                 1                 2
  STAGE IIA                3                 3
  STAGE IIA1               4                 1
  STAGE IIA2               1                 6
  STAGE IIB               17                10
  STAGE III                0                 1
  STAGE IIIB              14                20
  STAGE IVA                1                 2
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    27   7
  5Q GAIN WILD-TYPE 156  43
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               34               199 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                43 
$`5Q GAIN MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A7CM 
       31.40        46.32        57.73        20.91        40.93        20.35 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8YR TCGA-DG-A2KH 
      147.35        60.69         2.73        50.99        27.52         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-EA-A1QS TCGA-EA-A5O9 TCGA-EK-A2PG TCGA-EK-A2PM 
       58.88        44.94         0.76        13.91         1.51         0.59 
TCGA-EK-A2RN TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF 
        0.10         0.03        20.35         6.94        19.79         4.73 
TCGA-GH-A9DA TCGA-IR-A3LK TCGA-IR-A3LL TCGA-MY-A5BE TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        9.01        26.56        36.36         0.07        13.35        15.95 
TCGA-Q1-A6DT TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A958 
        3.39        12.16        14.07        43.82 

$`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       154.32 
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-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34        13.61        45.83         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KM 
       23.51         6.12        20.91         4.47        50.76        40.04 
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-A1QT 
       22.98        16.83        16.18        17.52         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-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        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       26.27         6.64         0.43         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         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-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-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        7.13        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        11.28         0.89         0.07         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
        0.20        13.87         0.03         5.42        29.72         4.34 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        5.49         2.96        15.58        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         5.88         6.25        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        93.99        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       20.22        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       23.24        44.88        42.58        42.08        39.35        38.96 
TCGA-WL-A834 
       18.05 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           147.35            195.85 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            17.87             15.58 
[1] "0.0 - 147.3 (17.9)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                 T1  T2 T3+T4
  5Q GAIN MUTATED    13   7     2
  5Q GAIN WILD-TYPE 108  43     9
D10V3, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                 13               108
  T2                  7                43
  T3+T4               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   15  5
  5Q GAIN WILD-TYPE 96 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     15    5
  5Q GAIN WILD-TYPE   96   42
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              15                96
  1               5                42
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED   15  0 10
  5Q GAIN WILD-TYPE 76  8 83
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              15                76
  M1               0                 8
  MX              10                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED               1                               31
  5Q GAIN WILD-TYPE             4                              166
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5Q GAIN MUTATED                                               1
  5Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5Q GAIN MUTATED                                     2
  5Q GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5Q GAIN MUTATED                                           0
  5Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5Q GAIN MUTATED                                              1
  5Q GAIN WILD-TYPE                                            5
D10V6, multiclass
                                               clus
vv                                              5Q GAIN MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           31
  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                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            166
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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     4  32
  5Q GAIN WILD-TYPE  26 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4   32
  5Q GAIN WILD-TYPE   26  176
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                4                26
  YES              32               176
[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                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED                           3
  5Q GAIN WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    29
  5Q GAIN WILD-TYPE                                         1   140
D10V10, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               3                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  29               140
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     2  20
  5Q GAIN WILD-TYPE  14 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2   20
  5Q GAIN WILD-TYPE   14  129
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              20               129
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   13  4
  5Q GAIN WILD-TYPE 58 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13    4
  5Q GAIN WILD-TYPE   58   21
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  TUMOR FREE              13                58
  WITH TUMOR               4                21
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  5Q GAIN MUTATED        2      3       0      1       1            29       0
  5Q GAIN WILD-TYPE     21      2       1      9       6           149      14
D10V14, multiclass
               clus
vv              5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  BRAZIL                      2                21
  CANADA                      3                 2
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     1                 6
  UNITED STATES              29               149
  VIETNAM                     0                14
[1] 7 2
[1] 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    3 13 17  0  3
  5Q GAIN WILD-TYPE 14 93 80  1 11
D10V15, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  G1               3                14
  G2              13                93
  G3              17                80
  G4               0                 1
  GX               3                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"
D10V16, continuous
D10V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5Q GAIN MUTATED                                             3
  5Q GAIN WILD-TYPE                                          28
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5Q GAIN MUTATED                9                  17
  5Q GAIN WILD-TYPE             43                  95
D10V18, multiclass
                                                 clus
vv                                                5Q 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                                                9
  LIFELONG NON-SMOKER                                          17
                                                 clus
vv                                                5Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 43
  LIFELONG NON-SMOKER                                            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"
D10V19, continuous
D10V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  5Q GAIN MUTATED             3       13             0        3
  5Q GAIN WILD-TYPE          16       62            12        9
D10V21, multiclass
               clus
vv              5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COMBINATION                 3                16
  EXTERNAL                   13                62
  EXTERNAL BEAM               0                12
  INTERNAL                    3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V22, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4  0
  5Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    0
  5Q GAIN WILD-TYPE   21    3
                         clus
vv                        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  4                21
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  5Q GAIN MUTATED                    0                0                   5
  5Q GAIN WILD-TYPE                  2                2                  23
                   vv
clus                REGIONAL SITE
  5Q GAIN MUTATED               3
  5Q GAIN WILD-TYPE            13
D10V23, multiclass
                     clus
vv                    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               5                23
  REGIONAL SITE                     3                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V24, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    7  0
  5Q GAIN WILD-TYPE 27  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7    0
  5Q GAIN WILD-TYPE   27    3
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CGY               7                27
  GY                0                 3
[1] 2 2
[1] FALSE
D10V25, continuous
D10V26, continuous
D10V27, continuous
D10V28, continuous
D10V29, continuous
D10V30, 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                       5
  5Q GAIN WILD-TYPE                                   4                      24
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5Q GAIN MUTATED                         0                       1
  5Q GAIN WILD-TYPE                       1                       6
D10V31, multiclass
                                     clus
vv                                    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 4
  OTHER LOCATION, SPECIFY                           5                24
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             16
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5Q GAIN MUTATED                                                                                  16
  5Q GAIN WILD-TYPE                                                                                52
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5Q GAIN MUTATED                                                                                             11
  5Q GAIN WILD-TYPE                                                                                           94
D10V32, 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)                         16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              11
                                                                                              clus
vv                                                                                             5Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              16
  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)                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V33, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   10  7
  5Q GAIN WILD-TYPE 58 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     10    7
  5Q GAIN WILD-TYPE   58   63
         clus
vv        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ABSENT               10                58
  PRESENT               7                63
[1] 2 2
[1] FALSE
D10V34, continuous
D10V35, continuous
D10V36, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4 15
  5Q GAIN WILD-TYPE 39 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4   15
  5Q GAIN WILD-TYPE   39   79
                                          clus
vv                                         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   4                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              15                79
[1] 2 2
[1] FALSE
D10V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5Q GAIN MUTATED              1           6          8
  5Q GAIN WILD-TYPE            9          43         49
D10V38, multiclass
              clus
vv             5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                6                43
  NEVER USED                 8                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"
D10V39, continuous
D10V40, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   14  0
  5Q GAIN WILD-TYPE 75 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     14    0
  5Q GAIN WILD-TYPE   75   16
         clus
vv        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ABSENT               14                75
  PRESENT               0                16
[1] 2 2
[1] FALSE
D10V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  5Q GAIN MUTATED     0    0   5    6    2  0   2    2    0   3  0   2  0   0
  5Q GAIN WILD-TYPE   1    1  25   59   22  4   6    5    9  19  1   6  2   1
                   vv
clus                TX
  5Q GAIN MUTATED    4
  5Q GAIN WILD-TYPE 10
D10V42, multiclass
      clus
vv     5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                5                25
  T1B1               6                59
  T1B2               2                22
  T2                 0                 4
  T2A                2                 6
  T2A1               2                 5
  T2A2               0                 9
  T2B                3                19
  T3                 0                 1
  T3B                2                 6
  T4                 0                 2
  TIS                0                 1
  TX                 4                10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  5Q GAIN MUTATED         1        0         0         0        2        12
  5Q GAIN WILD-TYPE       3        2         1         1       29        57
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  5Q GAIN MUTATED           5        0         2          1          0
  5Q GAIN WILD-TYPE        27        3         4          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  5Q GAIN MUTATED           5         0          5         0         0
  5Q GAIN WILD-TYPE        22         1         29         3         7
D10V44, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 2                29
  STAGE IB1               12                57
  STAGE IB2                5                27
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                5                22
  STAGE III                0                 1
  STAGE IIIB               5                29
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    30  13
  6P GAIN WILD-TYPE 153  37
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               43               190 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13                37 
$`6P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH 
       57.04         5.46        31.40        46.32        35.01        38.99 
TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CH 
       35.61        20.91        78.35        52.01        17.85       154.32 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-DS-A7WI TCGA-EA-A1QS 
       85.55        94.95         2.73        45.83         8.28         0.76 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2PM TCGA-EK-A2RA 
       14.50         1.81        14.96         0.36         0.59        16.08 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A57G TCGA-HG-A2PA TCGA-IR-A3LF TCGA-IR-A3LH 
        1.22        23.84         1.32        25.41        96.95        78.71 
TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MU-A5YI TCGA-MY-A913 
       10.06        30.31        11.28         0.07         0.03         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD TCGA-VS-A8EJ TCGA-VS-A8QH TCGA-VS-A952 
        2.96        13.35        11.67        19.96        39.78        44.88 
TCGA-VS-A959 
       39.35 

$`6P 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-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
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-A2LZ 
        3.58        44.22        73.18        73.45        83.05       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
       38.43         0.82        18.02        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        20.35       147.35        17.19        60.69 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34        13.61        50.99         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       58.88        50.76        44.94        40.04        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-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52        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-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 
       15.02        14.99        13.58        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         6.64         1.51         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.13         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-A3GK 
       23.70         2.24         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        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.12         4.73         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-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.97         1.12         9.01         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       117.40 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        20.48        15.58         5.13         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
      195.85         7.99         0.89         0.30         0.82         0.20 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       13.87         5.42        29.72         0.07         4.34        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        5.88         6.25        10.39        19.59         3.88        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       14.07        53.52        32.15        46.03        23.28        11.51 
TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 
       49.55        31.27        16.64         4.73        23.24        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       42.08        43.82        38.96        18.05 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.03              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           154.32            195.85 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            19.96             15.53 
[1] "0.0 - 154.3 (20.0)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.4"
D11V2, continuous
                   vv
clus                 T1  T2 T3+T4
  6P GAIN MUTATED    20  10     1
  6P GAIN WILD-TYPE 101  40    10
D11V3, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                 20               101
  T2                 10                40
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   21  6
  6P GAIN WILD-TYPE 90 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     21    6
  6P GAIN WILD-TYPE   90   41
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              21                90
  1               6                41
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6P GAIN MUTATED   17  2 15
  6P GAIN WILD-TYPE 74  6 78
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              17                74
  M1               2                 6
  MX              15                78
[1] 3 2
[1] 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                               35
  6P GAIN WILD-TYPE             5                              162
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6P GAIN MUTATED                                               1
  6P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6P GAIN MUTATED                                     4
  6P GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6P GAIN MUTATED                                           0
  6P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6P GAIN MUTATED                                              4
  6P GAIN WILD-TYPE                                            2
D11V6, multiclass
                                               clus
vv                                              6P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           35
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                4
                                               clus
vv                                              6P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            162
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  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     9  35
  6P GAIN WILD-TYPE  21 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9   35
  6P GAIN WILD-TYPE   21  173
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                9                21
  YES              35               173
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  1     5
  6P GAIN WILD-TYPE                                7    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED                           5
  6P GAIN WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           0    31
  6P GAIN WILD-TYPE                                         1   138
D11V10, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   5                13
  BLACK OR AFRICAN AMERICAN                               5                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  31               138
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3  28
  6P GAIN WILD-TYPE  13 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3   28
  6P GAIN WILD-TYPE   13  121
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              28               121
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   11 10
  6P GAIN WILD-TYPE 60 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     11   10
  6P GAIN WILD-TYPE   60   15
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  TUMOR FREE              11                60
  WITH TUMOR              10                15
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  6P GAIN MUTATED        4      0       1      1       2            32       4
  6P GAIN WILD-TYPE     19      5       0      9       5           146      10
D11V14, multiclass
               clus
vv              6P GAIN MUTATED 6P GAIN WILD-TYPE
  BRAZIL                      4                19
  CANADA                      0                 5
  NIGERIA                     1                 0
  RUSSIA                      1                 9
  UKRAINE                     2                 5
  UNITED STATES              32               146
  VIETNAM                     4                10
[1] 7 2
[1] 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 20 21  1  1
  6P GAIN WILD-TYPE 17 86 76  0 13
D11V15, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  G1               0                17
  G2              20                86
  G3              21                76
  G4               1                 0
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V16, continuous
D11V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6P GAIN MUTATED                                             4
  6P GAIN WILD-TYPE                                          27
                   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                                                 1
  6P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6P GAIN MUTATED               11                  23
  6P GAIN WILD-TYPE             41                  89
D11V18, multiclass
                                                 clus
vv                                                6P 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                                               11
  LIFELONG NON-SMOKER                                          23
                                                 clus
vv                                                6P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 41
  LIFELONG NON-SMOKER                                            89
[1] 5 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
D11V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  6P GAIN MUTATED             8       12             1        2
  6P GAIN WILD-TYPE          11       63            11       10
D11V21, multiclass
               clus
vv              6P GAIN MUTATED 6P GAIN WILD-TYPE
  COMBINATION                 8                11
  EXTERNAL                   12                63
  EXTERNAL BEAM               1                11
  INTERNAL                    2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V22, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    9  0
  6P GAIN WILD-TYPE 16  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9    0
  6P GAIN WILD-TYPE   16    3
                         clus
vv                        6P GAIN MUTATED 6P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  6P GAIN MUTATED                    0                0                   6
  6P GAIN WILD-TYPE                  2                2                  22
                   vv
clus                REGIONAL SITE
  6P GAIN MUTATED               1
  6P GAIN WILD-TYPE            15
D11V23, multiclass
                     clus
vv                    6P GAIN MUTATED 6P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               6                22
  REGIONAL SITE                     1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V24, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    5  1
  6P GAIN WILD-TYPE 29  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    1
  6P GAIN WILD-TYPE   29    2
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  CGY               5                29
  GY                1                 2
[1] 2 2
[1] FALSE
D11V25, continuous
D11V26, continuous
D11V27, continuous
D11V28, continuous
D11V29, continuous
D11V30, 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                       5
  6P GAIN WILD-TYPE                                   6                      24
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6P GAIN MUTATED                         0                       1
  6P GAIN WILD-TYPE                       1                       6
D11V31, multiclass
                                     clus
vv                                    6P GAIN MUTATED 6P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           5                24
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  6P 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                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6P GAIN MUTATED                                                                                  13
  6P GAIN WILD-TYPE                                                                                55
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6P GAIN MUTATED                                                                                             20
  6P GAIN WILD-TYPE                                                                                           85
D11V32, 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)                         13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              20
                                                                                              clus
vv                                                                                             6P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V33, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   13 10
  6P GAIN WILD-TYPE 55 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     13   10
  6P GAIN WILD-TYPE   55   60
         clus
vv        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ABSENT               13                55
  PRESENT              10                60
[1] 2 2
[1] FALSE
D11V34, continuous
D11V35, continuous
D11V36, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    6 16
  6P GAIN WILD-TYPE 37 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6   16
  6P GAIN WILD-TYPE   37   78
                                          clus
vv                                         6P GAIN MUTATED 6P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              16                78
[1] 2 2
[1] FALSE
D11V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6P GAIN MUTATED              0          11         10
  6P GAIN WILD-TYPE           10          38         47
D11V38, multiclass
              clus
vv             6P GAIN MUTATED 6P GAIN WILD-TYPE
  CURRENT USER               0                10
  FORMER USER               11                38
  NEVER USED                10                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"
D11V39, continuous
D11V40, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   11  4
  6P GAIN WILD-TYPE 78 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     11    4
  6P GAIN WILD-TYPE   78   12
         clus
vv        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ABSENT               11                78
  PRESENT               4                12
[1] 2 2
[1] FALSE
D11V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  6P GAIN MUTATED     0    1   3   12    4  1   1    3    2   3  0   1  0   1
  6P GAIN WILD-TYPE   1    0  27   53   20  3   7    4    7  19  1   7  2   0
                   vv
clus                TX
  6P GAIN MUTATED    2
  6P GAIN WILD-TYPE 12
D11V42, multiclass
      clus
vv     6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1A                0                 1
  T1A1               1                 0
  T1B                3                27
  T1B1              12                53
  T1B2               4                20
  T2                 1                 3
  T2A                1                 7
  T2A1               3                 4
  T2A2               2                 7
  T2B                3                19
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                1                 0
  TX                 2                12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  6P GAIN MUTATED         0        0         1         0        3        16
  6P GAIN WILD-TYPE       4        2         0         1       28        53
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  6P GAIN MUTATED           7        0         1          3          2
  6P GAIN WILD-TYPE        25        3         5          2          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  6P GAIN MUTATED           7         0          3         0         0
  6P GAIN WILD-TYPE        20         1         31         3         7
D11V44, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                 3                28
  STAGE IB1               16                53
  STAGE IB2                7                25
  STAGE II                 0                 3
  STAGE IIA                1                 5
  STAGE IIA1               3                 2
  STAGE IIA2               2                 5
  STAGE IIB                7                20
  STAGE III                0                 1
  STAGE IIIB               3                31
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    19  10
  6Q GAIN WILD-TYPE 164  40
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               29               204 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               10                40 
$`6Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI 
       57.04        31.40        46.32        35.01        38.99        35.61 
TCGA-C5-A1ML TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-C5-A8XH 
       20.91        52.01        17.85        85.55         2.73        45.83 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A97N TCGA-EK-A2PM 
        8.28         0.76        14.50         1.81         0.36         0.59 
TCGA-EK-A2RA TCGA-HG-A2PA TCGA-IR-A3LH TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q8 
       16.08        25.41        78.71        10.06         5.13        30.31 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-UC-A7PD TCGA-VS-A8QH TCGA-VS-A952 
        5.49         2.96        11.67        39.78        44.88 

$`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       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19        60.69        94.95         9.34        13.61 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99         8.35        75.78        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        6.12        20.91         4.47         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        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        17.52 
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-A44S TCGA-EA-A4BA 
        1.18        14.50         1.35         1.35        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        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        6.64         1.51         0.43         0.59         1.45         0.13 
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        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.73         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-GH-A9DA TCGA-HG-A9SC 
        1.35         1.32         1.97         1.12         9.01         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81       117.40        96.95        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        6.71        21.11       195.85         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         0.07         4.34        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        5.88         6.25        10.39        19.59         3.88        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       14.07        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       11.51        49.55        31.27        16.64         4.73        23.24 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.36              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            85.55            195.85 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            20.91             15.53 
[1] "0.4 - 85.5 (20.9)"  "0.0 - 195.8 (15.5)"
[1] "hr=" "1.8"
D12V2, continuous
                   vv
clus                 T1  T2 T3+T4
  6Q GAIN MUTATED    12   7     1
  6Q GAIN WILD-TYPE 109  43    10
D12V3, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                 12               109
  T2                  7                43
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   15  5
  6Q GAIN WILD-TYPE 96 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15    5
  6Q GAIN WILD-TYPE   96   42
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              15                96
  1               5                42
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6Q GAIN MUTATED   12  1  9
  6Q GAIN WILD-TYPE 79  7 84
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              12                79
  M1               1                 7
  MX               9                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED               0                               22
  6Q GAIN WILD-TYPE             5                              175
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6Q GAIN MUTATED                                               0
  6Q GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6Q GAIN MUTATED                                     3
  6Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6Q GAIN MUTATED                                           0
  6Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6Q GAIN MUTATED                                              4
  6Q GAIN WILD-TYPE                                            2
D12V6, multiclass
                                               clus
vv                                              6Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           22
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                4
                                               clus
vv                                              6Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            175
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  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     7  22
  6Q GAIN WILD-TYPE  23 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   22
  6Q GAIN WILD-TYPE   23  186
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                7                23
  YES              22               186
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  1     2
  6Q GAIN WILD-TYPE                                7    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED                           3
  6Q GAIN WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           0    22
  6Q GAIN WILD-TYPE                                         1   147
D12V10, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               3                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  22               147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     4  17
  6Q GAIN WILD-TYPE  12 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4   17
  6Q GAIN WILD-TYPE   12  132
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                12
  NOT HISPANIC OR LATINO              17               132
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    6  8
  6Q GAIN WILD-TYPE 65 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6    8
  6Q GAIN WILD-TYPE   65   17
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  TUMOR FREE               6                65
  WITH TUMOR               8                17
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  6Q GAIN MUTATED        2      0       1      1       2            22       1
  6Q GAIN WILD-TYPE     21      5       0      9       5           156      13
D12V14, multiclass
               clus
vv              6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  BRAZIL                      2                21
  CANADA                      0                 5
  NIGERIA                     1                 0
  RUSSIA                      1                 9
  UKRAINE                     2                 5
  UNITED STATES              22               156
  VIETNAM                     1                13
[1] 7 2
[1] 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 15 11  1  1
  6Q GAIN WILD-TYPE 17 91 86  0 13
D12V15, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  G1               0                17
  G2              15                91
  G3              11                86
  G4               1                 0
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V16, continuous
D12V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6Q GAIN MUTATED                                             4
  6Q GAIN WILD-TYPE                                          27
                   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                                                 1
  6Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6Q GAIN MUTATED                9                  12
  6Q GAIN WILD-TYPE             43                 100
D12V18, multiclass
                                                 clus
vv                                                6Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                9
  LIFELONG NON-SMOKER                                          12
                                                 clus
vv                                                6Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 43
  LIFELONG NON-SMOKER                                           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"
D12V19, continuous
D12V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  6Q GAIN MUTATED             6        6             1        2
  6Q GAIN WILD-TYPE          13       69            11       10
D12V21, multiclass
               clus
vv              6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COMBINATION                 6                13
  EXTERNAL                    6                69
  EXTERNAL BEAM               1                11
  INTERNAL                    2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V22, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    7  0
  6Q GAIN WILD-TYPE 18  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7    0
  6Q GAIN WILD-TYPE   18    3
                         clus
vv                        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  7                18
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  6Q GAIN MUTATED                    0                0                   4
  6Q GAIN WILD-TYPE                  2                2                  24
                   vv
clus                REGIONAL SITE
  6Q GAIN MUTATED               0
  6Q GAIN WILD-TYPE            16
D12V23, multiclass
                     clus
vv                    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               4                24
  REGIONAL SITE                     0                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V24, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    2  1
  6Q GAIN WILD-TYPE 32  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    1
  6Q GAIN WILD-TYPE   32    2
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CGY               2                32
  GY                1                 2
[1] 2 2
[1] FALSE
D12V25, continuous
D12V26, continuous
D12V27, continuous
D12V28, continuous
D12V29, continuous
D12V30, 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                       5
  6Q GAIN WILD-TYPE                                   6                      24
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6Q GAIN MUTATED                         0                       1
  6Q GAIN WILD-TYPE                       1                       6
D12V31, multiclass
                                     clus
vv                                    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           5                24
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  6Q 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                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6Q GAIN MUTATED                                                                                   7
  6Q GAIN WILD-TYPE                                                                                61
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6Q GAIN MUTATED                                                                                             16
  6Q GAIN WILD-TYPE                                                                                           89
D12V32, 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)                          7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              16
                                                                                              clus
vv                                                                                             6Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V33, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    8  7
  6Q GAIN WILD-TYPE 60 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8    7
  6Q GAIN WILD-TYPE   60   63
         clus
vv        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ABSENT                8                60
  PRESENT               7                63
[1] 2 2
[1] FALSE
D12V34, continuous
D12V35, continuous
D12V36, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    5 10
  6Q GAIN WILD-TYPE 38 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5   10
  6Q GAIN WILD-TYPE   38   84
                                          clus
vv                                         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              10                84
[1] 2 2
[1] FALSE
D12V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6Q GAIN MUTATED              0           7          7
  6Q GAIN WILD-TYPE           10          42         50
D12V38, multiclass
              clus
vv             6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CURRENT USER               0                10
  FORMER USER                7                42
  NEVER USED                 7                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"
D12V39, continuous
D12V40, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    7  3
  6Q GAIN WILD-TYPE 82 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7    3
  6Q GAIN WILD-TYPE   82   13
         clus
vv        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ABSENT                7                82
  PRESENT               3                13
[1] 2 2
[1] FALSE
D12V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  6Q GAIN MUTATED     0    0   3    6    3  0   1    2    2   2  0   1  0   1
  6Q GAIN WILD-TYPE   1    1  27   59   21  4   7    5    7  20  1   7  2   0
                   vv
clus                TX
  6Q GAIN MUTATED    1
  6Q GAIN WILD-TYPE 13
D12V42, multiclass
      clus
vv     6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                3                27
  T1B1               6                59
  T1B2               3                21
  T2                 0                 4
  T2A                1                 7
  T2A1               2                 5
  T2A2               2                 7
  T2B                2                20
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                1                 0
  TX                 1                13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  6Q GAIN MUTATED         0        0         0         0        3        10
  6Q GAIN WILD-TYPE       4        2         1         1       28        59
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  6Q GAIN MUTATED           5        0         1          2          2
  6Q GAIN WILD-TYPE        27        3         5          3          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  6Q GAIN MUTATED           5         0          1         0         0
  6Q GAIN WILD-TYPE        22         1         33         3         7
D12V44, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                28
  STAGE IB1               10                59
  STAGE IB2                5                27
  STAGE II                 0                 3
  STAGE IIA                1                 5
  STAGE IIA1               2                 3
  STAGE IIA2               2                 5
  STAGE IIB                5                22
  STAGE III                0                 1
  STAGE IIIB               1                33
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    22  10
  7P GAIN WILD-TYPE 161  40
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               32               201 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                40 
$`7P GAIN MUTATED`
TCGA-C5-A1BL TCGA-C5-A1MK TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A7CH 
      173.29         2.43        73.18        78.35       100.14       154.32 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8YQ TCGA-DG-A2KJ 
      147.35        17.19        60.69        94.95        23.51        58.88 
TCGA-EA-A50E TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.26        12.59         1.51         0.07         0.36         1.18 
TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A40J TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A69B 
        4.73        23.84         1.35        36.36        21.44        10.06 
TCGA-MY-A913 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8EJ 
        5.49         3.39        19.59        12.16        14.07        19.96 
TCGA-VS-A8QC TCGA-VS-A8QF 
       11.51        49.55 

$`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-A1ML TCGA-C5-A1MN 
       53.16        38.99        35.61         0.46        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 
        3.58        44.22        73.45        83.05        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-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 
      134.33        15.48        20.35        85.55         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52         6.12        20.91         4.47         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        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        17.52 
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-A556 TCGA-EA-A5FO 
       14.50         1.81        12.66        12.82        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
        0.36        45.96        26.27         6.64         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         1.45         0.13        16.08         4.04         0.03 
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-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
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-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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        26.56        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        24.56        20.48        15.58         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       195.85        30.31         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        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        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       13.35        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        5.88         6.25        10.39         3.88        11.67        93.99 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL 
       61.28        10.03        34.52        29.03        20.22        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       32.15        46.03        23.28        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           173.29            195.85 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            18.39             15.58 
[1] "0.1 - 173.3 (18.4)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                 T1  T2 T3+T4
  7P GAIN MUTATED    10   6     3
  7P GAIN WILD-TYPE 111  44     8
D13V3, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                 10               111
  T2                  6                44
  T3+T4               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    11   5
  7P GAIN WILD-TYPE 100  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11    5
  7P GAIN WILD-TYPE  100   42
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              11               100
  1               5                42
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   10  2 11
  7P GAIN WILD-TYPE 81  6 82
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              10                81
  M1               2                 6
  MX              11                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED               0                               30
  7P GAIN WILD-TYPE             5                              167
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7P GAIN MUTATED                                               0
  7P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7P GAIN MUTATED                                     2
  7P GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7P GAIN MUTATED                                           0
  7P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7P GAIN MUTATED                                              0
  7P GAIN WILD-TYPE                                            6
D13V6, multiclass
                                               clus
vv                                              7P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           30
  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                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            167
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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  28
  7P GAIN WILD-TYPE  26 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   28
  7P GAIN WILD-TYPE   26  180
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                4                26
  YES              28               180
[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                                7    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED                           4
  7P GAIN WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           0    25
  7P GAIN WILD-TYPE                                         1   144
D13V10, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               4                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  25               144
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     3  18
  7P GAIN WILD-TYPE  13 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3   18
  7P GAIN WILD-TYPE   13  131
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              18               131
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    8  6
  7P GAIN WILD-TYPE 63 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    6
  7P GAIN WILD-TYPE   63   19
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  TUMOR FREE               8                63
  WITH TUMOR               6                19
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  7P GAIN MUTATED        4      1       0      0       0            26       1
  7P GAIN WILD-TYPE     19      4       1     10       7           152      13
D13V14, multiclass
               clus
vv              7P GAIN MUTATED 7P GAIN WILD-TYPE
  BRAZIL                      4                19
  CANADA                      1                 4
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 7
  UNITED STATES              26               152
  VIETNAM                     1                13
[1] 7 2
[1] 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    1 12 16  0  3
  7P GAIN WILD-TYPE 16 94 81  1 11
D13V15, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  G1               1                16
  G2              12                94
  G3              16                81
  G4               0                 1
  GX               3                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"
D13V16, continuous
D13V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7P GAIN MUTATED                                             2
  7P GAIN WILD-TYPE                                          29
                   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                                                 1
  7P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7P GAIN MUTATED                7                  15
  7P GAIN WILD-TYPE             45                  97
D13V18, multiclass
                                                 clus
vv                                                7P GAIN 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                                                7
  LIFELONG NON-SMOKER                                          15
                                                 clus
vv                                                7P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 45
  LIFELONG NON-SMOKER                                            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"
D13V19, continuous
D13V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  7P GAIN MUTATED             3       12             1        3
  7P GAIN WILD-TYPE          16       63            11        9
D13V21, multiclass
               clus
vv              7P GAIN MUTATED 7P GAIN WILD-TYPE
  COMBINATION                 3                16
  EXTERNAL                   12                63
  EXTERNAL BEAM               1                11
  INTERNAL                    3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V22, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    3  1
  7P GAIN WILD-TYPE 22  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3    1
  7P GAIN WILD-TYPE   22    2
                         clus
vv                        7P GAIN MUTATED 7P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  3                22
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  7P GAIN MUTATED                    0                0                   7
  7P GAIN WILD-TYPE                  2                2                  21
                   vv
clus                REGIONAL SITE
  7P GAIN MUTATED               4
  7P GAIN WILD-TYPE            12
D13V23, multiclass
                     clus
vv                    7P GAIN MUTATED 7P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               7                21
  REGIONAL SITE                     4                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V24, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    7  2
  7P GAIN WILD-TYPE 27  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7    2
  7P GAIN WILD-TYPE   27    1
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  CGY               7                27
  GY                2                 1
[1] 2 2
[1] FALSE
D13V25, continuous
D13V26, continuous
D13V27, continuous
D13V28, continuous
D13V29, continuous
D13V30, 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                       2
  7P GAIN WILD-TYPE                                   6                      27
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7P GAIN MUTATED                         1                       0
  7P GAIN WILD-TYPE                       0                       7
D13V31, multiclass
                                     clus
vv                                    7P GAIN MUTATED 7P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           2                27
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  7P GAIN MUTATED                                               0
  7P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  7P GAIN MUTATED                                                2
  7P GAIN WILD-TYPE                                             14
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7P GAIN MUTATED                                                                                  11
  7P GAIN WILD-TYPE                                                                                57
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7P GAIN MUTATED                                                                                             12
  7P GAIN WILD-TYPE                                                                                           93
D13V32, multiclass
                                                                                              clus
vv                                                                                             7P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              12
                                                                                              clus
vv                                                                                             7P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V33, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    3  9
  7P GAIN WILD-TYPE 65 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3    9
  7P GAIN WILD-TYPE   65   61
         clus
vv        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ABSENT                3                65
  PRESENT               9                61
[1] 2 2
[1] FALSE
D13V34, continuous
D13V35, continuous
D13V36, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5 13
  7P GAIN WILD-TYPE 38 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   13
  7P GAIN WILD-TYPE   38   81
                                          clus
vv                                         7P GAIN MUTATED 7P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              13                81
[1] 2 2
[1] FALSE
D13V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7P GAIN MUTATED              1           3          4
  7P GAIN WILD-TYPE            9          46         53
D13V38, multiclass
              clus
vv             7P GAIN MUTATED 7P GAIN WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                3                46
  NEVER USED                 4                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"
D13V39, continuous
D13V40, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    8  2
  7P GAIN WILD-TYPE 81 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    2
  7P GAIN WILD-TYPE   81   14
         clus
vv        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ABSENT                8                81
  PRESENT               2                14
[1] 2 2
[1] FALSE
D13V41, continuous
[1] "Remove cluster labels:" "7P GAIN MUTATED"       
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  7P GAIN MUTATED     0    0   5    3    2  0   0    3    1   2  0   2  1   1
  7P GAIN WILD-TYPE   1    1  25   62   22  4   8    4    8  20  1   6  1   0
                   vv
clus                TX
  7P GAIN MUTATED    3
  7P GAIN WILD-TYPE 11
D13V42, multiclass
      clus
vv     7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                5                25
  T1B1               3                62
  T1B2               2                22
  T2                 0                 4
  T2A                0                 8
  T2A1               3                 4
  T2A2               1                 8
  T2B                2                20
  T3                 0                 1
  T3B                2                 6
  T4                 1                 1
  TIS                1                 0
  TX                 3                11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  7P GAIN MUTATED         1        0         0         0        4         5
  7P GAIN WILD-TYPE       3        2         1         1       27        64
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  7P GAIN MUTATED           3        0         2          1          0
  7P GAIN WILD-TYPE        29        3         4          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  7P GAIN MUTATED           5         0          7         2         1
  7P GAIN WILD-TYPE        22         1         27         1         6
D13V44, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                27
  STAGE IB1                5                64
  STAGE IB2                3                29
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                5                22
  STAGE III                0                 1
  STAGE IIIB               7                27
  STAGE IVA                2                 1
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    23   7
  7Q GAIN WILD-TYPE 160  43
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               30               203 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                43 
$`7Q GAIN MUTATED`
TCGA-C5-A1BL TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ 
      173.29        53.16         2.43        73.18        78.35       100.14 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8YQ TCGA-DG-A2KJ 
      147.35        17.19        60.69        94.95        23.51        58.88 
TCGA-DR-A0ZL TCGA-DS-A3LQ TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RJ 
       87.75        22.98        12.59         1.51         0.07         1.18 
TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3NI TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-A69B 
        4.73        23.84         1.45        36.36        20.48        10.06 
TCGA-MY-A913 TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A9U5 
        5.49        12.16        14.07        19.96        49.55        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       38.99        35.61         0.46        20.91        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-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       182.93       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 
      134.33        15.48        20.35        85.55         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52         6.12        20.91         4.47         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        40.04        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        17.52         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-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-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96        26.27         6.64         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45         0.13        16.08         4.04         0.03         0.36 
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-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        26.56        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        24.56        21.44        15.58         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       195.85        30.31         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        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        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       13.35        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         5.88         6.25        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        93.99        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       20.22        53.52        32.15        46.03        23.28        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        16.64         4.73        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        18.05 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           173.29            195.85 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           23.245            15.020 
[1] "0.1 - 173.3 (23.2)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                 T1  T2 T3+T4
  7Q GAIN MUTATED    13   4     3
  7Q GAIN WILD-TYPE 108  46     8
D14V3, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                 13               108
  T2                  4                46
  T3+T4               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    11   5
  7Q GAIN WILD-TYPE 100  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     11    5
  7Q GAIN WILD-TYPE  100   42
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              11               100
  1               5                42
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   10  2 10
  7Q GAIN WILD-TYPE 81  6 83
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              10                81
  M1               2                 6
  MX              10                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED               0                               29
  7Q GAIN WILD-TYPE             5                              168
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7Q GAIN MUTATED                                               0
  7Q GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7Q GAIN MUTATED                                     1
  7Q GAIN WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7Q GAIN MUTATED                                           0
  7Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7Q GAIN MUTATED                                              0
  7Q GAIN WILD-TYPE                                            6
D14V6, multiclass
                                               clus
vv                                              7Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           29
  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                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            168
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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  24
  7Q GAIN WILD-TYPE  24 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6   24
  7Q GAIN WILD-TYPE   24  184
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                6                24
  YES              24               184
[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                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED                           5
  7Q GAIN WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           0    22
  7Q GAIN WILD-TYPE                                         1   147
D14V10, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               5                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  22               147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2  16
  7Q GAIN WILD-TYPE  14 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2   16
  7Q GAIN WILD-TYPE   14  133
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              16               133
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    9  3
  7Q GAIN WILD-TYPE 62 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      9    3
  7Q GAIN WILD-TYPE   62   22
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  TUMOR FREE               9                62
  WITH TUMOR               3                22
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  7Q GAIN MUTATED        4      1       0      0       0            25       0
  7Q GAIN WILD-TYPE     19      4       1     10       7           153      14
D14V14, multiclass
               clus
vv              7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  BRAZIL                      4                19
  CANADA                      1                 4
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 7
  UNITED STATES              25               153
  VIETNAM                     0                14
[1] 7 2
[1] 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    1 10 17  0  2
  7Q GAIN WILD-TYPE 16 96 80  1 12
D14V15, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  G1               1                16
  G2              10                96
  G3              17                80
  G4               0                 1
  GX               2                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"
D14V16, continuous
D14V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7Q GAIN MUTATED                                             3
  7Q GAIN WILD-TYPE                                          28
                   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                                                 1
  7Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7Q GAIN MUTATED                7                  11
  7Q GAIN WILD-TYPE             45                 101
D14V18, multiclass
                                                 clus
vv                                                7Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                7
  LIFELONG NON-SMOKER                                          11
                                                 clus
vv                                                7Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 45
  LIFELONG NON-SMOKER                                           101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V19, continuous
D14V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  7Q GAIN MUTATED             4       11             2        3
  7Q GAIN WILD-TYPE          15       64            10        9
D14V21, multiclass
               clus
vv              7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COMBINATION                 4                15
  EXTERNAL                   11                64
  EXTERNAL BEAM               2                10
  INTERNAL                    3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V22, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5  1
  7Q GAIN WILD-TYPE 20  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    1
  7Q GAIN WILD-TYPE   20    2
                         clus
vv                        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  7Q GAIN MUTATED                    0                0                   7
  7Q GAIN WILD-TYPE                  2                2                  21
                   vv
clus                REGIONAL SITE
  7Q GAIN MUTATED               3
  7Q GAIN WILD-TYPE            13
D14V23, multiclass
                     clus
vv                    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               7                21
  REGIONAL SITE                     3                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V24, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7  1
  7Q GAIN WILD-TYPE 27  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7    1
  7Q GAIN WILD-TYPE   27    2
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CGY               7                27
  GY                1                 2
[1] 2 2
[1] FALSE
D14V25, continuous
D14V26, continuous
D14V27, continuous
D14V28, continuous
D14V29, continuous
D14V30, 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                       4
  7Q GAIN WILD-TYPE                                   6                      25
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7Q GAIN MUTATED                         0                       0
  7Q GAIN WILD-TYPE                       1                       7
D14V31, multiclass
                                     clus
vv                                    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           4                25
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  7Q GAIN MUTATED                                               0
  7Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  7Q GAIN MUTATED                                                1
  7Q GAIN WILD-TYPE                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7Q GAIN MUTATED                                                                                  10
  7Q GAIN WILD-TYPE                                                                                58
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7Q GAIN MUTATED                                                                                             13
  7Q GAIN WILD-TYPE                                                                                           92
D14V32, multiclass
                                                                                              clus
vv                                                                                             7Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              13
                                                                                              clus
vv                                                                                             7Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           58
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V33, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  8
  7Q GAIN WILD-TYPE 64 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    8
  7Q GAIN WILD-TYPE   64   62
         clus
vv        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ABSENT                4                64
  PRESENT               8                62
[1] 2 2
[1] FALSE
D14V34, continuous
D14V35, continuous
D14V36, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5 12
  7Q GAIN WILD-TYPE 38 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5   12
  7Q GAIN WILD-TYPE   38   82
                                          clus
vv                                         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              12                82
[1] 2 2
[1] FALSE
D14V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7Q GAIN MUTATED              1           4          6
  7Q GAIN WILD-TYPE            9          45         51
D14V38, multiclass
              clus
vv             7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                4                45
  NEVER USED                 6                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"
D14V39, continuous
D14V40, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7  1
  7Q GAIN WILD-TYPE 82 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7    1
  7Q GAIN WILD-TYPE   82   15
         clus
vv        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ABSENT                7                82
  PRESENT               1                15
[1] 2 2
[1] FALSE
D14V41, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"       
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  7Q GAIN MUTATED     0    0   4    5    4  0   0    2    0   2  0   3  0   1
  7Q GAIN WILD-TYPE   1    1  26   60   20  4   8    5    9  20  1   5  2   0
                   vv
clus                TX
  7Q GAIN MUTATED    1
  7Q GAIN WILD-TYPE 13
D14V42, multiclass
      clus
vv     7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                4                26
  T1B1               5                60
  T1B2               4                20
  T2                 0                 4
  T2A                0                 8
  T2A1               2                 5
  T2A2               0                 9
  T2B                2                20
  T3                 0                 1
  T3B                3                 5
  T4                 0                 2
  TIS                1                 0
  TX                 1                13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  7Q GAIN MUTATED         0        0         0         0        4         6
  7Q GAIN WILD-TYPE       4        2         1         1       27        63
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  7Q GAIN MUTATED           5        0         1          1          0
  7Q GAIN WILD-TYPE        27        3         5          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  7Q GAIN MUTATED           4         0          7         0         1
  7Q GAIN WILD-TYPE        23         1         27         3         6
D14V44, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                27
  STAGE IB1                6                63
  STAGE IB2                5                27
  STAGE II                 0                 3
  STAGE IIA                1                 5
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                4                23
  STAGE III                0                 1
  STAGE IIIB               7                27
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    30   9
  8P GAIN WILD-TYPE 153  41
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               194 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9                41 
$`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       154.32        60.69 
TCGA-C5-A8XI TCGA-C5-A8ZZ TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3Y4 TCGA-EA-A411 
        8.35        20.91        22.98         1.74        14.50         1.35 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A97N TCGA-EK-A2PM TCGA-EK-A2RN 
       12.82         0.26        13.91         0.36         0.59         0.10 
TCGA-EX-A8YF TCGA-FU-A3YQ TCGA-FU-A57G TCGA-IR-A3LL TCGA-JX-A3Q8 TCGA-MY-A5BF 
        4.73         3.52         1.32        36.36        30.31         4.34 
TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DW TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EJ 
        5.49        13.35        17.56        12.16        10.03        19.96 
TCGA-VS-A954 TCGA-VS-A958 TCGA-WL-A834 
       42.58        43.82        18.05 

$`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-A1ML 
       30.21        35.01        57.73         0.46         2.43        20.91 
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-A3HF TCGA-C5-A3HL 
      100.14        38.43         0.82        52.01        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       85.55        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83        75.78        99.91        23.51        27.52         6.12 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        4.47         1.12        58.88        50.76        44.94        40.04 
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        17.52         8.28         0.76        12.36 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 
        1.32         0.82         0.62        13.05         1.18         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       14.50         1.81        12.66        14.89         1.48        15.02 
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-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         6.64         1.51         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.18        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        19.79 
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-A40J 
        1.02         1.45         1.58         1.48         0.82         1.35 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        26.56        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU 
        5.13         6.71        21.11       195.85         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 
        0.03         5.42        29.72         0.07         2.96        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95         3.39        16.14        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        10.39        19.59         3.88        11.67        93.99 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL 
       61.28        34.52        29.03        20.22        14.07        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        23.28        11.51        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 
       31.27        16.64         4.73        23.24        44.88        42.08 
TCGA-VS-A959 TCGA-VS-A9U5 
       39.35        38.96 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           182.93            195.85 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            17.56             15.73 
[1] "0.1 - 182.9 (17.6)" "0.0 - 195.8 (15.7)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                 T1  T2 T3+T4
  8P GAIN MUTATED    18   7     5
  8P GAIN WILD-TYPE 103  43     6
D15V3, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                 18               103
  T2                  7                43
  T3+T4               5                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   19  8
  8P GAIN WILD-TYPE 92 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     19    8
  8P GAIN WILD-TYPE   92   39
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              19                92
  1               8                39
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED   14  3 15
  8P GAIN WILD-TYPE 77  5 78
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              14                77
  M1               3                 5
  MX              15                78
[1] 3 2
[1] 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                               36
  8P GAIN WILD-TYPE             5                              161
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8P GAIN MUTATED                                               0
  8P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8P GAIN MUTATED                                     3
  8P GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8P GAIN MUTATED                                           0
  8P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8P GAIN MUTATED                                              0
  8P GAIN WILD-TYPE                                            6
D15V6, multiclass
                                               clus
vv                                              8P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           36
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              8P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            161
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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  34
  8P GAIN WILD-TYPE  25 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5   34
  8P GAIN WILD-TYPE   25  174
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                5                25
  YES              34               174
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     2
  8P GAIN WILD-TYPE                                8    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED                           4
  8P GAIN WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0    31
  8P GAIN WILD-TYPE                                         1   138
D15V10, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               4                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  31               138
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1  26
  8P GAIN WILD-TYPE  15 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   26
  8P GAIN WILD-TYPE   15  123
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              26               123
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   12  4
  8P GAIN WILD-TYPE 59 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     12    4
  8P GAIN WILD-TYPE   59   21
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  TUMOR FREE              12                59
  WITH TUMOR               4                21
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  8P GAIN MUTATED        4      0       0      2       4            28       1
  8P GAIN WILD-TYPE     19      5       1      8       3           150      13
D15V14, multiclass
               clus
vv              8P GAIN MUTATED 8P GAIN WILD-TYPE
  BRAZIL                      4                19
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      2                 8
  UKRAINE                     4                 3
  UNITED STATES              28               150
  VIETNAM                     1                13
[1] 7 2
[1] 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    3 19 15  0  2
  8P GAIN WILD-TYPE 14 87 82  1 12
D15V15, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  G1               3                14
  G2              19                87
  G3              15                82
  G4               0                 1
  GX               2                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"
D15V16, continuous
D15V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8P GAIN MUTATED                                             5
  8P GAIN WILD-TYPE                                          26
                   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                                                 1
  8P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8P GAIN MUTATED                7                  22
  8P GAIN WILD-TYPE             45                  90
D15V18, multiclass
                                                 clus
vv                                                8P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                7
  LIFELONG NON-SMOKER                                          22
                                                 clus
vv                                                8P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 45
  LIFELONG NON-SMOKER                                            90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V19, continuous
D15V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  8P GAIN MUTATED             5       14             1        5
  8P GAIN WILD-TYPE          14       61            11        7
D15V21, multiclass
               clus
vv              8P GAIN MUTATED 8P GAIN WILD-TYPE
  COMBINATION                 5                14
  EXTERNAL                   14                61
  EXTERNAL BEAM               1                11
  INTERNAL                    5                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V22, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  0
  8P GAIN WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    0
  8P GAIN WILD-TYPE   20    3
                         clus
vv                        8P GAIN MUTATED 8P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  8P GAIN MUTATED                    0                0                   3
  8P GAIN WILD-TYPE                  2                2                  25
                   vv
clus                REGIONAL SITE
  8P GAIN MUTATED               4
  8P GAIN WILD-TYPE            12
D15V23, multiclass
                     clus
vv                    8P GAIN MUTATED 8P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               3                25
  REGIONAL SITE                     4                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V24, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    3  1
  8P GAIN WILD-TYPE 31  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    1
  8P GAIN WILD-TYPE   31    2
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  CGY               3                31
  GY                1                 2
[1] 2 2
[1] FALSE
D15V25, continuous
D15V26, continuous
D15V27, continuous
D15V28, continuous
D15V29, continuous
D15V30, 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                       7
  8P GAIN WILD-TYPE                                   6                      22
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8P GAIN MUTATED                         1                       1
  8P GAIN WILD-TYPE                       0                       6
D15V31, multiclass
                                     clus
vv                                    8P GAIN MUTATED 8P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           7                22
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8P GAIN MUTATED                                                                                  13
  8P GAIN WILD-TYPE                                                                                55
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8P GAIN MUTATED                                                                                             20
  8P GAIN WILD-TYPE                                                                                           85
D15V32, 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)                         13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              20
                                                                                              clus
vv                                                                                             8P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V33, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   10 13
  8P GAIN WILD-TYPE 58 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     10   13
  8P GAIN WILD-TYPE   58   57
         clus
vv        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ABSENT               10                58
  PRESENT              13                57
[1] 2 2
[1] FALSE
D15V34, continuous
D15V35, continuous
D15V36, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9 17
  8P GAIN WILD-TYPE 34 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   17
  8P GAIN WILD-TYPE   34   77
                                          clus
vv                                         8P GAIN MUTATED 8P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   9                34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              17                77
[1] 2 2
[1] FALSE
D15V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8P GAIN MUTATED              0          10          8
  8P GAIN WILD-TYPE           10          39         49
D15V38, multiclass
              clus
vv             8P GAIN MUTATED 8P GAIN WILD-TYPE
  CURRENT USER               0                10
  FORMER USER               10                39
  NEVER USED                 8                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"
D15V39, continuous
D15V40, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   13  2
  8P GAIN WILD-TYPE 76 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     13    2
  8P GAIN WILD-TYPE   76   14
         clus
vv        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ABSENT               13                76
  PRESENT               2                14
[1] 2 2
[1] FALSE
D15V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  8P GAIN MUTATED     0    0   3    7    8  1   1    1    1   3  0   4  1   1
  8P GAIN WILD-TYPE   1    1  27   58   16  3   7    6    8  19  1   4  1   0
                   vv
clus                TX
  8P GAIN MUTATED    2
  8P GAIN WILD-TYPE 12
D15V42, multiclass
      clus
vv     8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                3                27
  T1B1               7                58
  T1B2               8                16
  T2                 1                 3
  T2A                1                 7
  T2A1               1                 6
  T2A2               1                 8
  T2B                3                19
  T3                 0                 1
  T3B                4                 4
  T4                 1                 1
  TIS                1                 0
  TX                 2                12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  8P GAIN MUTATED         1        0         0         0        5         7
  8P GAIN WILD-TYPE       3        2         1         1       26        62
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  8P GAIN MUTATED           8        1         1          0          1
  8P GAIN WILD-TYPE        24        2         5          5          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  8P GAIN MUTATED           5         0          7         1         0
  8P GAIN WILD-TYPE        22         1         27         2         7
D15V44, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 5                26
  STAGE IB1                7                62
  STAGE IB2                8                24
  STAGE II                 1                 2
  STAGE IIA                1                 5
  STAGE IIA1               0                 5
  STAGE IIA2               1                 6
  STAGE IIB                5                22
  STAGE III                0                 1
  STAGE IIIB               7                27
  STAGE IVA                1                 2
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    52  13
  8Q GAIN WILD-TYPE 131  37
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               65               168 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13                37 
$`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-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8ZZ 
      154.32        60.69        50.99         8.35        23.51        20.91 
TCGA-DG-A2KJ TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3Y4 TCGA-EA-A411 
       58.88       117.99        22.98         1.74        14.50         1.35 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A97N TCGA-EK-A2H0 
       12.82         0.26        14.89        13.91         0.36        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        6.64         1.51         0.59         0.10         0.07         0.03 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A57G 
        6.12         4.73        23.84         1.45         3.52         1.32 
TCGA-HG-A9SC TCGA-IR-A3LL TCGA-JW-A852 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX 
        7.13        36.36         5.13        30.31        11.28         0.07 
TCGA-MU-A5YI TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW 
        0.03         4.34         5.49        13.35         3.39        17.56 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
       10.39        19.59         3.88        12.16        10.03        34.52 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A954 TCGA-VS-A958 TCGA-WL-A834 
       20.22        19.96        42.58        43.82        18.05 

$`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-A1ML 
       30.21        35.01        57.73         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
       40.93        44.22        73.18        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
        0.82        52.01        17.85        20.42       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34        13.61         2.73        45.83        75.78        99.91 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       27.52         6.12         4.47         1.12        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN 
       40.04        87.75        58.88        36.76         2.66       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28         0.76        12.36 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 
        1.32         0.82         0.62        13.05         1.18         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       14.50         1.81        12.66         1.48        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PL 
       14.96        13.58        13.48        12.59        26.27         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A3GJ 
        0.03         0.36         1.18        23.70         2.24         0.10 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10        20.35         7.92         6.94        14.70        19.79 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
        1.22         0.92         2.17         0.66         1.02         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        1.48         0.82         1.35         1.97         1.12         9.01 
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         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58        10.06         6.71        21.11       195.85         7.99 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM 
        0.89         0.30         0.82         0.20        13.87         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
       29.72         0.07         2.96        15.58        15.95        16.14 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-UC-A7PD TCGA-UC-A7PF 
       14.07        15.88         5.88         6.25        11.67        93.99 
TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       61.28        29.03        14.07        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       23.28        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
        4.73        23.24        44.88        42.08        39.35        38.96 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           182.93            195.85 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           14.500            16.015 
[1] "0.0 - 182.9 (14.5)" "0.0 - 195.8 (16.0)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                T1 T2 T3+T4
  8Q GAIN MUTATED   31 11     7
  8Q GAIN WILD-TYPE 90 39     4
D16V3, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                 31                90
  T2                 11                39
  T3+T4               7                 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"
D16V4, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   28 15
  8Q GAIN WILD-TYPE 83 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     28   15
  8Q GAIN WILD-TYPE   83   32
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              28                83
  1              15                32
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   24  3 25
  8Q GAIN WILD-TYPE 67  5 68
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              24                67
  M1               3                 5
  MX              25                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED               2                               60
  8Q GAIN WILD-TYPE             3                              137
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8Q GAIN MUTATED                                               0
  8Q GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8Q GAIN MUTATED                                     3
  8Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8Q GAIN MUTATED                                           1
  8Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8Q GAIN MUTATED                                              0
  8Q GAIN WILD-TYPE                                            6
D16V6, multiclass
                                               clus
vv                                              8Q GAIN MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           60
  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                                              8Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 3
  CERVICAL SQUAMOUS CELL CARCINOMA                            137
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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     6  60
  8Q GAIN WILD-TYPE  24 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6   60
  8Q GAIN WILD-TYPE   24  148
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                6                24
  YES              60               148
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1     4
  8Q GAIN WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED                           7
  8Q GAIN WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0    50
  8Q GAIN WILD-TYPE                                         1   119
D16V10, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                               7                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  50               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"
D16V11, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3  43
  8Q GAIN WILD-TYPE  13 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3   43
  8Q GAIN WILD-TYPE   13  106
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              43               106
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   20  6
  8Q GAIN WILD-TYPE 51 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     20    6
  8Q GAIN WILD-TYPE   51   19
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  TUMOR FREE              20                51
  WITH TUMOR               6                19
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  8Q GAIN MUTATED        6      1       0      3       4            49       3
  8Q GAIN WILD-TYPE     17      4       1      7       3           129      11
D16V14, multiclass
               clus
vv              8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  BRAZIL                      6                17
  CANADA                      1                 4
  NIGERIA                     0                 1
  RUSSIA                      3                 7
  UKRAINE                     4                 3
  UNITED STATES              49               129
  VIETNAM                     3                11
[1] 7 2
[1] 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    4 28 30  0  4
  8Q GAIN WILD-TYPE 13 78 67  1 10
D16V15, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  G1               4                13
  G2              28                78
  G3              30                67
  G4               0                 1
  GX               4                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"
D16V16, continuous
D16V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8Q GAIN MUTATED                                             8
  8Q GAIN WILD-TYPE                                          23
                   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                                                 1
  8Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8Q GAIN MUTATED               14                  30
  8Q GAIN WILD-TYPE             38                  82
D16V18, multiclass
                                                 clus
vv                                                8Q GAIN 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                                               14
  LIFELONG NON-SMOKER                                          30
                                                 clus
vv                                                8Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 38
  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"
D16V19, continuous
D16V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  8Q GAIN MUTATED             5       24             2        5
  8Q GAIN WILD-TYPE          14       51            10        7
D16V21, multiclass
               clus
vv              8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COMBINATION                 5                14
  EXTERNAL                   24                51
  EXTERNAL BEAM               2                10
  INTERNAL                    5                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V22, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5  1
  8Q GAIN WILD-TYPE 20  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    1
  8Q GAIN WILD-TYPE   20    2
                         clus
vv                        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  8Q GAIN MUTATED                    0                0                   7
  8Q GAIN WILD-TYPE                  2                2                  21
                   vv
clus                REGIONAL SITE
  8Q GAIN MUTATED               6
  8Q GAIN WILD-TYPE            10
D16V23, multiclass
                     clus
vv                    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               7                21
  REGIONAL SITE                     6                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V24, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    7  2
  8Q GAIN WILD-TYPE 27  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      7    2
  8Q GAIN WILD-TYPE   27    1
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CGY               7                27
  GY                2                 1
[1] 2 2
[1] FALSE
D16V25, continuous
D16V26, continuous
D16V27, continuous
D16V28, continuous
D16V29, continuous
D16V30, 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                      10
  8Q GAIN WILD-TYPE                                   6                      19
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8Q GAIN MUTATED                         1                       1
  8Q GAIN WILD-TYPE                       0                       6
D16V31, multiclass
                                     clus
vv                                    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                          10                19
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  8Q GAIN MUTATED                                               1
  8Q GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8Q GAIN MUTATED                                                5
  8Q GAIN WILD-TYPE                                             11
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8Q GAIN MUTATED                                                                                  23
  8Q GAIN WILD-TYPE                                                                                45
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8Q GAIN MUTATED                                                                                             29
  8Q GAIN WILD-TYPE                                                                                           76
D16V32, multiclass
                                                                                              clus
vv                                                                                             8Q GAIN 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)              29
                                                                                              clus
vv                                                                                             8Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V33, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14 19
  8Q GAIN WILD-TYPE 54 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14   19
  8Q GAIN WILD-TYPE   54   51
         clus
vv        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ABSENT               14                54
  PRESENT              19                51
[1] 2 2
[1] FALSE
D16V34, continuous
D16V35, continuous
D16V36, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   12 30
  8Q GAIN WILD-TYPE 31 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     12   30
  8Q GAIN WILD-TYPE   31   64
                                          clus
vv                                         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  12                31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              30                64
[1] 2 2
[1] FALSE
D16V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8Q GAIN MUTATED              0          14         12
  8Q GAIN WILD-TYPE           10          35         45
D16V38, multiclass
              clus
vv             8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CURRENT USER               0                10
  FORMER USER               14                35
  NEVER USED                12                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"
D16V39, continuous
D16V40, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   19  4
  8Q GAIN WILD-TYPE 70 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     19    4
  8Q GAIN WILD-TYPE   70   12
         clus
vv        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ABSENT               19                70
  PRESENT               4                12
[1] 2 2
[1] FALSE
D16V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  8Q GAIN MUTATED     0    1   7   14    9  2   1    2    1   5  0   6  1   1
  8Q GAIN WILD-TYPE   1    0  23   51   15  2   7    5    8  17  1   2  1   0
                   vv
clus                TX
  8Q GAIN MUTATED    4
  8Q GAIN WILD-TYPE 10
D16V42, multiclass
      clus
vv     8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1A                0                 1
  T1A1               1                 0
  T1B                7                23
  T1B1              14                51
  T1B2               9                15
  T2                 2                 2
  T2A                1                 7
  T2A1               2                 5
  T2A2               1                 8
  T2B                5                17
  T3                 0                 1
  T3B                6                 2
  T4                 1                 1
  TIS                1                 0
  TX                 4                10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  8Q GAIN MUTATED         2        0         1         1        8        14
  8Q GAIN WILD-TYPE       2        2         0         0       23        55
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  8Q GAIN MUTATED           9        1         1          1          1
  8Q GAIN WILD-TYPE        23        2         5          4          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  8Q GAIN MUTATED          10         0         13         1         0
  8Q GAIN WILD-TYPE        17         1         21         2         7
D16V44, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                 0                 2
  STAGE IA1                1                 0
  STAGE IA2                1                 0
  STAGE IB                 8                23
  STAGE IB1               14                55
  STAGE IB2                9                23
  STAGE II                 1                 2
  STAGE IIA                1                 5
  STAGE IIA1               1                 4
  STAGE IIA2               1                 6
  STAGE IIB               10                17
  STAGE III                0                 1
  STAGE IIIB              13                21
  STAGE IVA                1                 2
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    29   9
  9P GAIN WILD-TYPE 154  41
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               38               195 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                9                41 
$`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-DG-A2KL TCGA-DG-A2KM 
       15.48       147.35        85.55         2.73        44.94        40.04 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A5ZE TCGA-EK-A2H1 TCGA-EK-A2RN TCGA-EX-A3L1 
       22.98        16.83        14.99        26.27         0.10         6.94 
TCGA-FU-A3TX TCGA-FU-A40J TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JW-A69B 
        1.48         1.35        36.36        27.42        15.58        10.06 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE TCGA-MY-A913 
       21.11        30.31        11.28         0.30         0.07         5.49 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QC 
       11.67        12.16        20.22        53.52        32.15        11.51 
TCGA-VS-A94X TCGA-VS-A9U5 
       16.64        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       20.91        40.93        44.22        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
       38.43        52.01        18.02        17.85        20.42       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      101.82        20.35        17.19        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       58.88        50.76        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
      117.99       118.65        16.18        17.52         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-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-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       15.02        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         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-A449 TCGA-EX-A69L 
        0.10         0.03        20.35         7.92        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        6.12         4.73         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-A3YQ 
        0.66         1.02         1.45         1.58         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        24.56        21.44        20.48         5.13         6.71 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU 
      195.85         7.99         0.89         0.07         0.82         0.20 
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 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        3.88        93.99        61.28        10.03        34.52        29.03 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       14.07        19.96        46.03        23.28        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       31.27         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.07              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           182.93            195.85 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           16.735            15.580 
[1] "0.1 - 182.9 (16.7)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1"  
D17V2, continuous
                   vv
clus                 T1  T2 T3+T4
  9P GAIN MUTATED    16  11     3
  9P GAIN WILD-TYPE 105  39     8
D17V3, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1                 16               105
  T2                 11                39
  T3+T4               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   14 10
  9P GAIN WILD-TYPE 97 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     14   10
  9P GAIN WILD-TYPE   97   37
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              14                97
  1              10                37
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9P GAIN MUTATED   14  1 17
  9P GAIN WILD-TYPE 77  7 76
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              14                77
  M1               1                 7
  MX              17                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED               0                               33
  9P GAIN WILD-TYPE             5                              164
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9P GAIN MUTATED                                               1
  9P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9P GAIN MUTATED                                     4
  9P GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9P GAIN MUTATED                                           0
  9P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9P GAIN MUTATED                                              1
  9P GAIN WILD-TYPE                                            5
D17V6, multiclass
                                               clus
vv                                              9P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           33
  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                                              9P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            164
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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  37
  9P GAIN WILD-TYPE  28 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   37
  9P GAIN WILD-TYPE   28  171
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2                28
  YES              37               171
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  3     4
  9P GAIN WILD-TYPE                                5    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED                           6
  9P GAIN WILD-TYPE                        18
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    21
  9P GAIN WILD-TYPE                                         1   148
D17V10, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 5
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                               6                18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  21               148
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     4  16
  9P GAIN WILD-TYPE  12 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4   16
  9P GAIN WILD-TYPE   12  133
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                12
  NOT HISPANIC OR LATINO              16               133
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   13  0
  9P GAIN WILD-TYPE 58 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     13    0
  9P GAIN WILD-TYPE   58   25
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  TUMOR FREE              13                58
  WITH TUMOR               0                25
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  9P GAIN MUTATED        6      2       0      0       0            28       3
  9P GAIN WILD-TYPE     17      3       1     10       7           150      11
D17V14, multiclass
               clus
vv              9P GAIN MUTATED 9P GAIN WILD-TYPE
  BRAZIL                      6                17
  CANADA                      2                 3
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 7
  UNITED STATES              28               150
  VIETNAM                     3                11
[1] 7 2
[1] 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    3 17 18  0  1
  9P GAIN WILD-TYPE 14 89 79  1 13
D17V15, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  G1               3                14
  G2              17                89
  G3              18                79
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V16, continuous
D17V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9P GAIN MUTATED                                             2
  9P GAIN WILD-TYPE                                          29
                   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                                                 2
  9P GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9P GAIN MUTATED               11                  19
  9P GAIN WILD-TYPE             41                  93
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               2
  CURRENT SMOKER                                               11
  LIFELONG NON-SMOKER                                          19
                                                 clus
vv                                                9P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 41
  LIFELONG NON-SMOKER                                            93
[1] 5 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
D17V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  9P GAIN MUTATED             0       16             2        5
  9P GAIN WILD-TYPE          19       59            10        7
D17V21, multiclass
               clus
vv              9P GAIN MUTATED 9P GAIN WILD-TYPE
  COMBINATION                 0                19
  EXTERNAL                   16                59
  EXTERNAL BEAM               2                10
  INTERNAL                    5                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V22, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  0
  9P GAIN WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    0
  9P GAIN WILD-TYPE   23    3
                         clus
vv                        9P GAIN MUTATED 9P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  9P GAIN MUTATED                    0                0                   9
  9P GAIN WILD-TYPE                  2                2                  19
                   vv
clus                REGIONAL SITE
  9P GAIN MUTATED               6
  9P GAIN WILD-TYPE            10
D17V23, multiclass
                     clus
vv                    9P GAIN MUTATED 9P GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               9                19
  REGIONAL SITE                     6                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V24, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   11  2
  9P GAIN WILD-TYPE 23  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     11    2
  9P GAIN WILD-TYPE   23    1
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  CGY              11                23
  GY                2                 1
[1] 2 2
[1] FALSE
D17V25, continuous
D17V26, continuous
D17V27, continuous
D17V28, continuous
D17V29, continuous
D17V30, 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                       7
  9P GAIN WILD-TYPE                                   6                      22
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9P GAIN MUTATED                         0                       1
  9P GAIN WILD-TYPE                       1                       6
D17V31, multiclass
                                     clus
vv                                    9P GAIN MUTATED 9P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           7                22
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  9P GAIN MUTATED                                               0
  9P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9P GAIN MUTATED                                                4
  9P GAIN WILD-TYPE                                             12
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9P GAIN MUTATED                                                                                   8
  9P GAIN WILD-TYPE                                                                                60
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9P GAIN MUTATED                                                                                             19
  9P GAIN WILD-TYPE                                                                                           86
D17V32, multiclass
                                                                                              clus
vv                                                                                             9P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              19
                                                                                              clus
vv                                                                                             9P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V33, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   10 12
  9P GAIN WILD-TYPE 58 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     10   12
  9P GAIN WILD-TYPE   58   58
         clus
vv        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ABSENT               10                58
  PRESENT              12                58
[1] 2 2
[1] FALSE
D17V34, continuous
D17V35, continuous
D17V36, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   10  9
  9P GAIN WILD-TYPE 33 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     10    9
  9P GAIN WILD-TYPE   33   85
                                          clus
vv                                         9P GAIN MUTATED 9P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               9                85
[1] 2 2
[1] FALSE
D17V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9P GAIN MUTATED              2           8          8
  9P GAIN WILD-TYPE            8          41         49
D17V38, multiclass
              clus
vv             9P GAIN MUTATED 9P GAIN WILD-TYPE
  CURRENT USER               2                 8
  FORMER USER                8                41
  NEVER USED                 8                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"
D17V39, continuous
D17V40, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   12  0
  9P GAIN WILD-TYPE 77 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     12    0
  9P GAIN WILD-TYPE   77   16
         clus
vv        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ABSENT               12                77
  PRESENT               0                16
[1] 2 2
[1] FALSE
D17V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  9P GAIN MUTATED     0    0   6    6    4  1   4    2    0   4  0   3  0   1
  9P GAIN WILD-TYPE   1    1  24   59   20  3   4    5    9  18  1   5  2   0
                   vv
clus                TX
  9P GAIN MUTATED    1
  9P GAIN WILD-TYPE 13
D17V42, multiclass
      clus
vv     9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                6                24
  T1B1               6                59
  T1B2               4                20
  T2                 1                 3
  T2A                4                 4
  T2A1               2                 5
  T2A2               0                 9
  T2B                4                18
  T3                 0                 1
  T3B                3                 5
  T4                 0                 2
  TIS                1                 0
  TX                 1                13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  9P GAIN MUTATED         0        0         0         0        6        10
  9P GAIN WILD-TYPE       4        2         1         1       25        59
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  9P GAIN MUTATED           7        0         3          1          0
  9P GAIN WILD-TYPE        25        3         3          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  9P GAIN MUTATED           3         0          7         2         0
  9P GAIN WILD-TYPE        24         1         27         1         7
D17V44, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 6                25
  STAGE IB1               10                59
  STAGE IB2                7                25
  STAGE II                 0                 3
  STAGE IIA                3                 3
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                3                24
  STAGE III                0                 1
  STAGE IIIB               7                27
  STAGE IVA                2                 1
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    27   8
  9Q GAIN WILD-TYPE 156  42
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               35               198 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8                42 
$`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-C5-A8ZZ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A3LQ 
      147.35        85.55        20.91        44.94        40.04        22.98 
TCGA-EA-A5ZE TCGA-EK-A2H1 TCGA-EK-A2PM TCGA-EK-A2RN TCGA-EX-A3L1 TCGA-FU-A3TX 
       14.99        26.27         0.59         0.10         6.94         1.48 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JW-A852 
        3.52         1.35        36.36        27.42        15.58         5.13 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A6DT TCGA-UC-A7PD 
       11.28         0.30         0.07         5.49         3.39        11.67 
TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A94X 
       12.16        20.22        32.15        11.51        16.64 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       20.91        40.93        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-A7CH TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI 
      154.32       101.82        20.35        17.19        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 
       75.78        99.91        23.51        27.52         6.12         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        58.88        50.76        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        17.52 
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-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
        1.48        13.91        15.02        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
        0.36        12.59        45.96         6.64         1.51         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         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-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH 
        3.29        24.56        21.44        20.48        10.06         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85        30.31         7.99         0.89         0.07 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.82         0.20        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-A6DV 
        4.34         2.96        15.58        13.35        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59         3.88        93.99        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA 
       29.03        14.07        19.96        53.52        46.03        23.28 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       49.55        39.78        31.27         4.73        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.07              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           182.93            195.85 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           15.480            16.015 
[1] "0.1 - 182.9 (15.5)" "0.0 - 195.8 (16.0)"
[1] "hr=" "1"  
D18V2, continuous
                   vv
clus                 T1  T2 T3+T4
  9Q GAIN MUTATED    14   9     3
  9Q GAIN WILD-TYPE 107  41     8
D18V3, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1                 14               107
  T2                  9                41
  T3+T4               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   13 10
  9Q GAIN WILD-TYPE 98 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     13   10
  9Q GAIN WILD-TYPE   98   37
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              13                98
  1              10                37
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9Q GAIN MUTATED   12  1 16
  9Q GAIN WILD-TYPE 79  7 77
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              12                79
  M1               1                 7
  MX              16                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED               0                               35
  9Q GAIN WILD-TYPE             5                              162
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9Q GAIN MUTATED                                               1
  9Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9Q GAIN MUTATED                                     1
  9Q GAIN WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9Q GAIN MUTATED                                           0
  9Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9Q GAIN MUTATED                                              0
  9Q GAIN WILD-TYPE                                            6
D18V6, multiclass
                                               clus
vv                                              9Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           35
  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                                              9Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            162
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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  35
  9Q GAIN WILD-TYPE  28 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   35
  9Q GAIN WILD-TYPE   28  173
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                2                28
  YES              35               173
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  3     4
  9Q GAIN WILD-TYPE                                5    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED                           5
  9Q GAIN WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    20
  9Q GAIN WILD-TYPE                                         1   149
D18V10, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 5
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                               5                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  20               149
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     4  16
  9Q GAIN WILD-TYPE  12 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4   16
  9Q GAIN WILD-TYPE   12  133
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                12
  NOT HISPANIC OR LATINO              16               133
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   11  1
  9Q GAIN WILD-TYPE 60 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11    1
  9Q GAIN WILD-TYPE   60   24
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  TUMOR FREE              11                60
  WITH TUMOR               1                24
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  9Q GAIN MUTATED        4      2       0      0       0            27       4
  9Q GAIN WILD-TYPE     19      3       1     10       7           151      10
D18V14, multiclass
               clus
vv              9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  BRAZIL                      4                19
  CANADA                      2                 3
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 7
  UNITED STATES              27               151
  VIETNAM                     4                10
[1] 7 2
[1] 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    4 16 16  0  1
  9Q GAIN WILD-TYPE 13 90 81  1 13
D18V15, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  G1               4                13
  G2              16                90
  G3              16                81
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V16, continuous
D18V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9Q GAIN MUTATED                                             1
  9Q GAIN WILD-TYPE                                          30
                   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                                                 2
  9Q GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9Q GAIN MUTATED               11                  17
  9Q GAIN WILD-TYPE             41                  95
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               2
  CURRENT SMOKER                                               11
  LIFELONG NON-SMOKER                                          17
                                                 clus
vv                                                9Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 41
  LIFELONG NON-SMOKER                                            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"
D18V19, continuous
D18V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  9Q GAIN MUTATED             0       12             2        6
  9Q GAIN WILD-TYPE          19       63            10        6
D18V21, multiclass
               clus
vv              9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COMBINATION                 0                19
  EXTERNAL                   12                63
  EXTERNAL BEAM               2                10
  INTERNAL                    6                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V22, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  0
  9Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    0
  9Q GAIN WILD-TYPE   23    3
                         clus
vv                        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  9Q GAIN MUTATED                    0                0                   7
  9Q GAIN WILD-TYPE                  2                2                  21
                   vv
clus                REGIONAL SITE
  9Q GAIN MUTATED               7
  9Q GAIN WILD-TYPE             9
D18V23, multiclass
                     clus
vv                    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               7                21
  REGIONAL SITE                     7                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V24, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    9  2
  9Q GAIN WILD-TYPE 25  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9    2
  9Q GAIN WILD-TYPE   25    1
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CGY               9                25
  GY                2                 1
[1] 2 2
[1] FALSE
D18V25, continuous
D18V26, continuous
D18V27, continuous
D18V28, continuous
D18V29, continuous
D18V30, 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                       6
  9Q GAIN WILD-TYPE                                   6                      23
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9Q GAIN MUTATED                         0                       1
  9Q GAIN WILD-TYPE                       1                       6
D18V31, multiclass
                                     clus
vv                                    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           6                23
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  9Q GAIN MUTATED                                               0
  9Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9Q GAIN MUTATED                                                3
  9Q GAIN WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9Q GAIN MUTATED                                                                                   8
  9Q GAIN WILD-TYPE                                                                                60
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9Q GAIN MUTATED                                                                                             18
  9Q GAIN WILD-TYPE                                                                                           87
D18V32, multiclass
                                                                                              clus
vv                                                                                             9Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              18
                                                                                              clus
vv                                                                                             9Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V33, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    9  9
  9Q GAIN WILD-TYPE 59 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9    9
  9Q GAIN WILD-TYPE   59   61
         clus
vv        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ABSENT                9                59
  PRESENT               9                61
[1] 2 2
[1] FALSE
D18V34, continuous
D18V35, continuous
D18V36, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   10 12
  9Q GAIN WILD-TYPE 33 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10   12
  9Q GAIN WILD-TYPE   33   82
                                          clus
vv                                         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              12                82
[1] 2 2
[1] FALSE
D18V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9Q GAIN MUTATED              2           6          5
  9Q GAIN WILD-TYPE            8          43         52
D18V38, multiclass
              clus
vv             9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CURRENT USER               2                 8
  FORMER USER                6                43
  NEVER USED                 5                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"
D18V39, continuous
D18V40, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    9  0
  9Q GAIN WILD-TYPE 80 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9    0
  9Q GAIN WILD-TYPE   80   16
         clus
vv        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ABSENT                9                80
  PRESENT               0                16
[1] 2 2
[1] FALSE
D18V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  9Q GAIN MUTATED     0    0   6    5    3  1   3    2    0   3  0   3  0   1
  9Q GAIN WILD-TYPE   1    1  24   60   21  3   5    5    9  19  1   5  2   0
                   vv
clus                TX
  9Q GAIN MUTATED    2
  9Q GAIN WILD-TYPE 12
D18V42, multiclass
      clus
vv     9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                6                24
  T1B1               5                60
  T1B2               3                21
  T2                 1                 3
  T2A                3                 5
  T2A1               2                 5
  T2A2               0                 9
  T2B                3                19
  T3                 0                 1
  T3B                3                 5
  T4                 0                 2
  TIS                1                 0
  TX                 2                12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  9Q GAIN MUTATED         1        0         0         0        6         8
  9Q GAIN WILD-TYPE       3        2         1         1       25        61
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  9Q GAIN MUTATED           5        0         3          1          0
  9Q GAIN WILD-TYPE        27        3         3          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  9Q GAIN MUTATED           4         0          7         2         0
  9Q GAIN WILD-TYPE        23         1         27         1         7
D18V44, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 6                25
  STAGE IB1                8                61
  STAGE IB2                5                27
  STAGE II                 0                 3
  STAGE IIA                3                 3
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                4                23
  STAGE III                0                 1
  STAGE IIIB               7                27
  STAGE IVA                2                 1
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    14   6
  10P GAIN WILD-TYPE 169  44
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                213 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                 44 
$`10P GAIN MUTATED`
TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7X5 
      173.29        35.01        57.73       100.14       154.32        13.61 
TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DS-A0VK TCGA-EA-A97N TCGA-EK-A2PG 
       45.83        23.51         1.12        36.76         0.36         1.51 
TCGA-EK-A2RJ TCGA-FU-A3NI TCGA-GH-A9DA TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-LP-A4AW 
        1.18         1.45         9.01        14.93        36.36         0.89 
TCGA-VS-A8EI TCGA-VS-A9U5 
       14.07        38.96 

$`10P 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-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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        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        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
       85.55        60.69        94.95         9.34         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        75.78        99.91        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        4.47        58.88        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88         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        17.52         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        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        6.64         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       16.08         0.07         4.04         0.03         0.36        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        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.73         1.22        23.84         0.92         2.17         0.66 
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-HG-A9SC TCGA-HM-A3JJ 
        1.32         1.97         1.12        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78         9.44       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-A5VH 
       96.95        78.71        81.96        26.56        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        6.71        21.11       195.85        30.31         7.99        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
        5.42        29.72         0.07         4.34         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
        3.88        11.67        93.99        12.16        61.28        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       34.52        29.03        20.22        19.96        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       46.03        23.28        11.51        49.55        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.36               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            173.29             195.85 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             19.22              15.88 
[1] "0.4 - 173.3 (19.2)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                  T1  T2 T3+T4
  10P GAIN MUTATED    12   1     2
  10P GAIN WILD-TYPE 109  49     9
D19V3, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                  12                109
  T2                   1                 49
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     8   5
  10P GAIN WILD-TYPE 103  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    5
  10P GAIN WILD-TYPE  103   42
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                8                103
  1                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10P GAIN MUTATED    9  0  6
  10P GAIN WILD-TYPE 82  8 87
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                9                 82
  M1                0                  8
  MX                6                 87
[1] 3 2
[1] 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               1                               17
  10P GAIN WILD-TYPE             4                              180
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10P GAIN MUTATED                                               0
  10P GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10P GAIN MUTATED                                     2
  10P GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10P GAIN MUTATED                                           0
  10P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10P GAIN MUTATED                                              0
  10P GAIN WILD-TYPE                                            6
D19V6, multiclass
                                               clus
vv                                              10P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  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                 0
                                               clus
vv                                              10P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             180
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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  18
  10P GAIN WILD-TYPE  28 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   18
  10P GAIN WILD-TYPE   28  190
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                 28
  YES               18                190
[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                                8    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED                           2
  10P GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           0    16
  10P GAIN WILD-TYPE                                         1   153
D19V10, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                2                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                153
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  15
  10P GAIN WILD-TYPE  16 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   15
  10P GAIN WILD-TYPE   16  134
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               15                134
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    5  2
  10P GAIN WILD-TYPE 66 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    2
  10P GAIN WILD-TYPE   66   23
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  TUMOR FREE                5                 66
  WITH TUMOR                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  10P GAIN MUTATED        2      1       0      0       1            15       1
  10P GAIN WILD-TYPE     21      4       1     10       6           163      13
D19V14, multiclass
               clus
vv              10P GAIN MUTATED 10P GAIN WILD-TYPE
  BRAZIL                       2                 21
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      1                  6
  UNITED STATES               15                163
  VIETNAM                      1                 13
[1] 7 2
[1] 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  7  8  0  2
  10P GAIN WILD-TYPE 15 99 89  1 12
D19V15, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  G1                2                 15
  G2                7                 99
  G3                8                 89
  G4                0                  1
  GX                2                 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"
D19V16, continuous
D19V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10P GAIN MUTATED                                             5
  10P GAIN WILD-TYPE                                          26
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10P GAIN MUTATED                4                   7
  10P GAIN WILD-TYPE             48                 105
D19V18, multiclass
                                                 clus
vv                                                10P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                            7
                                                 clus
vv                                                10P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  48
  LIFELONG NON-SMOKER                                            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"
D19V19, continuous
D19V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  10P GAIN MUTATED             1        7             2        0
  10P GAIN WILD-TYPE          18       68            10       12
D19V21, multiclass
               clus
vv              10P GAIN MUTATED 10P GAIN WILD-TYPE
  COMBINATION                  1                 18
  EXTERNAL                     7                 68
  EXTERNAL BEAM                2                 10
  INTERNAL                     0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V22, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  0
  10P GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    0
  10P GAIN WILD-TYPE   23    3
                         clus
vv                        10P GAIN MUTATED 10P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   2                 23
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  10P GAIN MUTATED                    0                0                   6
  10P GAIN WILD-TYPE                  2                2                  22
                    vv
clus                 REGIONAL SITE
  10P GAIN MUTATED               0
  10P GAIN WILD-TYPE            16
D19V23, multiclass
                     clus
vv                    10P GAIN MUTATED 10P GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                6                 22
  REGIONAL SITE                      0                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V24, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  0
  10P GAIN WILD-TYPE 30  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    0
  10P GAIN WILD-TYPE   30    3
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  CGY                4                 30
  GY                 0                  3
[1] 2 2
[1] FALSE
D19V25, continuous
D19V26, continuous
D19V27, continuous
D19V28, continuous
D19V29, continuous
D19V30, 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                         4                       0
  10P GAIN WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10P GAIN MUTATED                         1
  10P GAIN WILD-TYPE                       6
D19V31, multiclass
                                     clus
vv                                    10P GAIN MUTATED 10P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            4                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  10P GAIN MUTATED                                               0
  10P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  10P GAIN MUTATED                                                2
  10P GAIN WILD-TYPE                                             14
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10P GAIN MUTATED                                                                                   4
  10P GAIN WILD-TYPE                                                                                64
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10P GAIN MUTATED                                                                                              9
  10P GAIN WILD-TYPE                                                                                           96
D19V32, multiclass
                                                                                              clus
vv                                                                                             10P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                9
                                                                                              clus
vv                                                                                             10P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V33, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  7
  10P GAIN WILD-TYPE 64 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    7
  10P GAIN WILD-TYPE   64   63
         clus
vv        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ABSENT                 4                 64
  PRESENT                7                 63
[1] 2 2
[1] FALSE
D19V34, continuous
D19V35, continuous
D19V36, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    7  4
  10P GAIN WILD-TYPE 36 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7    4
  10P GAIN WILD-TYPE   36   90
                                          clus
vv                                         10P GAIN MUTATED 10P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    7                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                4                 90
[1] 2 2
[1] FALSE
D19V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10P GAIN MUTATED              0           3          5
  10P GAIN WILD-TYPE           10          46         52
D19V38, multiclass
              clus
vv             10P GAIN MUTATED 10P GAIN WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 3                 46
  NEVER USED                  5                 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"
D19V39, continuous
D19V40, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    9  0
  10P GAIN WILD-TYPE 80 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9    0
  10P GAIN WILD-TYPE   80   16
         clus
vv        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ABSENT                 9                 80
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D19V41, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  10P GAIN MUTATED     0    0   3    6    3  0   0    0    0   1  0   2  0   0
  10P GAIN WILD-TYPE   1    1  27   59   21  4   8    7    9  21  1   6  2   1
                    vv
clus                 TX
  10P GAIN MUTATED    0
  10P GAIN WILD-TYPE 14
D19V42, multiclass
      clus
vv     10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 3                 27
  T1B1                6                 59
  T1B2                3                 21
  T2                  0                  4
  T2A                 0                  8
  T2A1                0                  7
  T2A2                0                  9
  T2B                 1                 21
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  10P GAIN MUTATED         0        1         0         0        2         8
  10P GAIN WILD-TYPE       4        1         1         1       29        61
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  10P GAIN MUTATED           2        0         0          0          0
  10P GAIN WILD-TYPE        30        3         6          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  10P GAIN MUTATED           3         0          2         0         1
  10P GAIN WILD-TYPE        24         1         32         3         6
D19V44, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  1                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  2                 29
  STAGE IB1                 8                 61
  STAGE IB2                 2                 30
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 3                 24
  STAGE III                 0                  1
  STAGE IIIB                2                 32
  STAGE IVA                 0                  3
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     8   4
  10Q GAIN WILD-TYPE 175  46
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                221 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 46 
$`10Q GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A8XH TCGA-C5-A8YQ 
       35.01        57.73       100.14       154.32        45.83        23.51 
TCGA-DG-A2KH TCGA-EA-A97N TCGA-EK-A2PG TCGA-IR-A3LL TCGA-LP-A4AU TCGA-VS-A8EI 
        1.12         0.36         1.51        36.36        11.28        14.07 

$`10Q 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-A1MF 
       19.86        67.46        31.40        46.32        30.21        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-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        20.35       147.35 
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-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR 
        2.73        50.99         8.35        75.78        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
        6.12        20.91         4.47        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        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        17.52         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-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
       12.59        45.96        26.27         6.64         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         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-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-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        26.56        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        5.13         6.71        21.11       195.85        30.31         7.99 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
        0.03         5.42        29.72         0.07         4.34         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59         3.88        11.67        93.99        12.16        61.28 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        34.52        29.03        20.22        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        23.28        11.51        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       31.27        16.64         4.73        23.24        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.08        43.82        39.35        38.96        18.05 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.36               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            154.32             195.85 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             29.26              15.58 
[1] "0.4 - 154.3 (29.3)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                  T1  T2 T3+T4
  10Q GAIN MUTATED     5   1     2
  10Q GAIN WILD-TYPE 116  49     9
D20V3, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                   5                116
  T2                   1                 49
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5   2
  10Q GAIN WILD-TYPE 106  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    2
  10Q GAIN WILD-TYPE  106   45
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                5                106
  1                2                 45
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10Q GAIN MUTATED    7  0  1
  10Q GAIN WILD-TYPE 84  8 92
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                7                 84
  M1                0                  8
  MX                1                 92
[1] 3 2
[1] 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               1                                9
  10Q GAIN WILD-TYPE             4                              188
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10Q GAIN MUTATED                                               0
  10Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10Q GAIN MUTATED                                     2
  10Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10Q GAIN MUTATED                                           0
  10Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10Q GAIN MUTATED                                              0
  10Q GAIN WILD-TYPE                                            6
D20V6, multiclass
                                               clus
vv                                              10Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                             9
  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                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             188
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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  11
  10Q GAIN WILD-TYPE  29 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   11
  10Q GAIN WILD-TYPE   29  197
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                 29
  YES               11                197
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     1
  10Q GAIN WILD-TYPE                                8    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED                           1
  10Q GAIN WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           0     9
  10Q GAIN WILD-TYPE                                         1   160
D20V10, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                1                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                160
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   8
  10Q GAIN WILD-TYPE  16 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    8
  10Q GAIN WILD-TYPE   16  141
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO                8                141
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    4  2
  10Q GAIN WILD-TYPE 67 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4    2
  10Q GAIN WILD-TYPE   67   23
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  TUMOR FREE                4                 67
  WITH TUMOR                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  10Q GAIN MUTATED        1      1       0      0       1             8       1
  10Q GAIN WILD-TYPE     22      4       1     10       6           170      13
D20V14, multiclass
               clus
vv              10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  BRAZIL                       1                 22
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      1                  6
  UNITED STATES                8                170
  VIETNAM                      1                 13
[1] 7 2
[1] 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   5   3   0   2
  10Q GAIN WILD-TYPE  16 101  94   1  12
D20V15, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  G1                1                 16
  G2                5                101
  G3                3                 94
  G4                0                  1
  GX                2                 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"
D20V16, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 32 
        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-C5-A907         TCGA-DG-A2KK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EK-A2RA         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-JX-A3Q0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-VS-A8QF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-WL-A834 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10Q GAIN MUTATED                                             3
  10Q GAIN WILD-TYPE                                          28
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10Q GAIN MUTATED                2                   6
  10Q GAIN WILD-TYPE             50                 106
D20V18, multiclass
                                                 clus
vv                                                10Q 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                                                 2
  LIFELONG NON-SMOKER                                            6
                                                 clus
vv                                                10Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  50
  LIFELONG NON-SMOKER                                            106
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V19, continuous
D20V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  10Q GAIN MUTATED             0        5             1        0
  10Q GAIN WILD-TYPE          19       70            11       12
D20V21, multiclass
               clus
vv              10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COMBINATION                  0                 19
  EXTERNAL                     5                 70
  EXTERNAL BEAM                1                 11
  INTERNAL                     0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V22, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    1  0
  10Q GAIN WILD-TYPE 24  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    0
  10Q GAIN WILD-TYPE   24    3
                         clus
vv                        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   1                 24
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  10Q GAIN MUTATED                    0                0                   3
  10Q GAIN WILD-TYPE                  2                2                  25
                    vv
clus                 REGIONAL SITE
  10Q GAIN MUTATED               0
  10Q GAIN WILD-TYPE            16
D20V23, multiclass
                     clus
vv                    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                3                 25
  REGIONAL SITE                      0                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V24, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  0
  10Q GAIN WILD-TYPE 32  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    0
  10Q GAIN WILD-TYPE   32    3
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CGY                2                 32
  GY                 0                  3
[1] 2 2
[1] FALSE
D20V25, continuous
D20V26, continuous
D20V27, continuous
D20V28, continuous
D20V29, continuous
D20V30, 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                         3                       0
  10Q GAIN WILD-TYPE                      26                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10Q GAIN MUTATED                         0
  10Q GAIN WILD-TYPE                       7
D20V31, multiclass
                                     clus
vv                                    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            3                 26
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             16
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10Q GAIN MUTATED                                                                                   4
  10Q GAIN WILD-TYPE                                                                                64
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10Q GAIN MUTATED                                                                                              6
  10Q GAIN WILD-TYPE                                                                                           99
D20V32, 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)                           4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                6
                                                                                              clus
vv                                                                                             10Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V33, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  2
  10Q GAIN WILD-TYPE 65 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    2
  10Q GAIN WILD-TYPE   65   68
         clus
vv        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ABSENT                 3                 65
  PRESENT                2                 68
[1] 2 2
[1] FALSE
D20V34, continuous
D20V35, continuous
D20V36, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  1
  10Q GAIN WILD-TYPE 40 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    1
  10Q GAIN WILD-TYPE   40   93
                                          clus
vv                                         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                 93
[1] 2 2
[1] FALSE
D20V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10Q GAIN MUTATED              0           2          2
  10Q GAIN WILD-TYPE           10          47         55
D20V38, multiclass
              clus
vv             10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 2                 47
  NEVER USED                  2                 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"
D20V39, continuous
D20V40, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    5  0
  10Q GAIN WILD-TYPE 84 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    0
  10Q GAIN WILD-TYPE   84   16
         clus
vv        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ABSENT                 5                 84
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D20V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  10Q GAIN MUTATED     0    0   0    4    1  1   0    0    0   0  0   2  0   0
  10Q GAIN WILD-TYPE   1    1  30   61   23  3   8    7    9  22  1   6  2   1
                    vv
clus                 TX
  10Q GAIN MUTATED    0
  10Q GAIN WILD-TYPE 14
D20V42, multiclass
      clus
vv     10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 0                 30
  T1B1                4                 61
  T1B2                1                 23
  T2                  1                  3
  T2A                 0                  8
  T2A1                0                  7
  T2A2                0                  9
  T2B                 0                 22
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  10Q GAIN MUTATED         0        0         0         0        0         6
  10Q GAIN WILD-TYPE       4        2         1         1       31        63
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  10Q GAIN MUTATED           1        0         0          0          0
  10Q GAIN WILD-TYPE        31        3         6          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  10Q GAIN MUTATED           2         0          2         0         0
  10Q GAIN WILD-TYPE        25         1         32         3         7
D20V44, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  0                 31
  STAGE IB1                 6                 63
  STAGE IB2                 1                 31
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 2                 25
  STAGE III                 0                  1
  STAGE IIIB                2                 32
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     5   2
  11P GAIN WILD-TYPE 178  48
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                226 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 48 
$`11P GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-EK-A2H1 TCGA-FU-A40J TCGA-MY-A913 TCGA-VS-A8EC 
       35.01        73.18        26.27         1.35         5.49        34.52 
TCGA-VS-A8Q8 
       32.15 

$`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-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
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-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       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        4.47         1.12        58.88        50.76        44.94        40.04 
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        17.52         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-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-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
       12.59        45.96         6.64         1.51         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         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-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-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       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        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        5.13         6.71        21.11       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89         0.07         0.30         0.82         0.20 
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        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59         3.88        11.67        93.99        12.16        61.28 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        29.03        20.22        14.07        19.96        53.52 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       46.03        23.28        11.51        49.55        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.35               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             73.18             195.85 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             32.15              15.58 
[1] "1.4 - 73.2 (32.1)"  "0.0 - 195.8 (15.6)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                  T1  T2 T3+T4
  11P GAIN MUTATED     2   1     2
  11P GAIN WILD-TYPE 119  49     9
D21V3, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   2                119
  T2                   1                 49
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3   2
  11P GAIN WILD-TYPE 108  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    2
  11P GAIN WILD-TYPE  108   45
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                3                108
  1                2                 45
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11P GAIN MUTATED    3  1  2
  11P GAIN WILD-TYPE 88  7 91
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                3                 88
  M1                1                  7
  MX                2                 91
[1] 3 2
[1] 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                                6
  11P GAIN WILD-TYPE             5                              191
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11P GAIN MUTATED                                               0
  11P GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11P GAIN MUTATED                                     2
  11P GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11P GAIN MUTATED                                           0
  11P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11P GAIN MUTATED                                              0
  11P GAIN WILD-TYPE                                            6
D21V6, multiclass
                                               clus
vv                                              11P 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                                              11P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             191
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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   6
  11P GAIN WILD-TYPE  28 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    6
  11P GAIN WILD-TYPE   28  202
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 2                 28
  YES                6                202
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 72 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         TCGA-HM-A4S6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-AAVH         TCGA-JX-A3Q0         TCGA-MU-A5YI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PG         TCGA-VS-A8EH         TCGA-VS-A8QM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A94Y         TCGA-VS-A94Z         TCGA-WL-A834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED                           1
  11P GAIN WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           0     7
  11P GAIN WILD-TYPE                                         1   162
D21V10, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 18
  BLACK OR AFRICAN AMERICAN                                1                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                162
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   3
  11P GAIN WILD-TYPE  15 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    3
  11P GAIN WILD-TYPE   15  146
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO                3                146
[1] 2 2
[1] FALSE
D21V12, continuous
D21V13, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  1
  11P GAIN WILD-TYPE 70 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    1
  11P GAIN WILD-TYPE   70   24
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  TUMOR FREE                1                 70
  WITH TUMOR                1                 24
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  11P GAIN MUTATED        2      0       0      0       0             6       0
  11P GAIN WILD-TYPE     21      5       1     10       7           172      14
D21V14, multiclass
               clus
vv              11P GAIN MUTATED 11P GAIN WILD-TYPE
  BRAZIL                       2                 21
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  7
  UNITED STATES                6                172
  VIETNAM                      0                 14
[1] 7 2
[1] 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   3   5   0   0
  11P GAIN WILD-TYPE  17 103  92   1  14
D21V15, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  G1                0                 17
  G2                3                103
  G3                5                 92
  G4                0                  1
  GX                0                 14
[1] 5 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                 72 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         TCGA-HM-A4S6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-AAVH         TCGA-JX-A3Q0         TCGA-MU-A5YI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PG         TCGA-VS-A8EH         TCGA-VS-A8QM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A94Y         TCGA-VS-A94Z         TCGA-WL-A834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11P GAIN MUTATED                                             0
  11P GAIN WILD-TYPE                                          31
                    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                                                 1
  11P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11P GAIN MUTATED                1                   3
  11P GAIN WILD-TYPE             51                 109
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                1
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                            3
                                                 clus
vv                                                11P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  51
  LIFELONG NON-SMOKER                                            109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V19, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 66 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A8XI         TCGA-C5-A8YQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8YT         TCGA-C5-A8ZZ         TCGA-C5-A907 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EK-A2RA         TCGA-EX-A1H5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3TX         TCGA-FU-A3WB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A4S6         TCGA-HM-A6W2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VK         TCGA-JW-AAVH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-MU-A5YI         TCGA-MU-A8JM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73Q         TCGA-Q1-A73S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A8EH         TCGA-VS-A8QF         TCGA-VS-A8QM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A94Y         TCGA-VS-A94Z         TCGA-WL-A834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  11P GAIN MUTATED             0        2             2        1
  11P GAIN WILD-TYPE          19       73            10       11
D21V21, multiclass
               clus
vv              11P GAIN MUTATED 11P GAIN WILD-TYPE
  COMBINATION                  0                 19
  EXTERNAL                     2                 73
  EXTERNAL BEAM                2                 10
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V22, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  0
  11P GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    0
  11P GAIN WILD-TYPE   23    3
                         clus
vv                        11P GAIN MUTATED 11P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   2                 23
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  11P GAIN MUTATED                    0                0                   1
  11P GAIN WILD-TYPE                  2                2                  27
                    vv
clus                 REGIONAL SITE
  11P GAIN MUTATED               2
  11P GAIN WILD-TYPE            14
D21V23, multiclass
                     clus
vv                    11P GAIN MUTATED 11P GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                1                 27
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V24, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  1
  11P GAIN WILD-TYPE 32  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    1
  11P GAIN WILD-TYPE   32    2
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  CGY                2                 32
  GY                 1                  2
[1] 2 2
[1] FALSE
D21V25, continuous
D21V26, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                101 
        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-A1ML 
"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-A7X3         TCGA-C5-A7X8         TCGA-C5-A8ZZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DG-A2KL         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-A5VH         TCGA-JW-A5VI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-JX-A3PZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PG         TCGA-UC-A7PI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V27, continuous
D21V28, continuous
D21V29, continuous
D21V30, 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-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-A1ML 
"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-A7X3         TCGA-C5-A7X8         TCGA-C5-A8ZZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DG-A2KL         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-A5VH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VJ         TCGA-JW-A5VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VL         TCGA-JW-A69B         TCGA-JW-A852 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A3PZ         TCGA-JX-A3Q0         TCGA-JX-A3Q8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-Q1-A73Q         TCGA-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF         TCGA-UC-A7PG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PI 
"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                         2                       0
  11P GAIN WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11P GAIN MUTATED                         0
  11P GAIN WILD-TYPE                       7
D21V31, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 43 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1M5         TCGA-C5-A1M7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MJ         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-A2M1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HL         TCGA-C5-A7CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7UC         TCGA-C5-A7X8         TCGA-C5-A7XC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8XH         TCGA-C5-A8XI         TCGA-DG-A2KL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A8QA 
"11P GAIN WILD-TYPE" 
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  11P GAIN MUTATED                                               0
  11P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11P GAIN MUTATED                                                1
  11P GAIN WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11P GAIN MUTATED                                                                                   0
  11P GAIN WILD-TYPE                                                                                68
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11P GAIN MUTATED                                                                                              6
  11P GAIN WILD-TYPE                                                                                           99
D21V32, multiclass
                                                                                              clus
vv                                                                                             11P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           0
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                6
                                                                                              clus
vv                                                                                             11P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V33, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  2
  11P GAIN WILD-TYPE 65 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    2
  11P GAIN WILD-TYPE   65   68
         clus
vv        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ABSENT                 3                 65
  PRESENT                2                 68
[1] 2 2
[1] FALSE
D21V34, continuous
D21V35, continuous
D21V36, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  1
  11P GAIN WILD-TYPE 42 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    1
  11P GAIN WILD-TYPE   42   93
                                          clus
vv                                         11P GAIN MUTATED 11P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                 93
[1] 2 2
[1] FALSE
D21V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11P GAIN MUTATED              1           3          0
  11P GAIN WILD-TYPE            9          46         57
D21V38, multiclass
              clus
vv             11P GAIN MUTATED 11P GAIN WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 3                 46
  NEVER USED                  0                 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"
D21V39, continuous
D21V40, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 86 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    0
  11P GAIN WILD-TYPE   86   16
         clus
vv        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ABSENT                 3                 86
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D21V41, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A3JK         TCGA-JW-A852 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-MU-A51Y         TCGA-MU-A8JM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  11P GAIN MUTATED     0    0   2    0    0  0   0    1    0   0  0   2  0   1
  11P GAIN WILD-TYPE   1    1  28   65   24  4   8    6    9  22  1   6  2   0
                    vv
clus                 TX
  11P GAIN MUTATED    0
  11P GAIN WILD-TYPE 14
D21V42, multiclass
      clus
vv     11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 2                 28
  T1B1                0                 65
  T1B2                0                 24
  T2                  0                  4
  T2A                 0                  8
  T2A1                1                  6
  T2A2                0                  9
  T2B                 0                 22
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 1                  0
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  11P GAIN MUTATED         0        0         0         0        2         1
  11P GAIN WILD-TYPE       4        2         1         1       29        68
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  11P GAIN MUTATED           1        0         1          0          0
  11P GAIN WILD-TYPE        31        3         5          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  11P GAIN MUTATED           0         0          3         0         0
  11P GAIN WILD-TYPE        27         1         31         3         7
D21V44, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  2                 29
  STAGE IB1                 1                 68
  STAGE IB2                 1                 31
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 0                 27
  STAGE III                 0                  1
  STAGE IIIB                3                 31
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     6   1
  11Q GAIN WILD-TYPE 177  49
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                226 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 49 
$`11Q GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-DG-A2KJ TCGA-EK-A2H1 TCGA-EK-A2RJ TCGA-FU-A40J 
       35.01        73.18        58.88        26.27         1.18         1.35 
TCGA-MY-A913 
        5.49 

$`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-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
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-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       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        4.47         1.12        50.76        44.94        40.04        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        17.52         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        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.99        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36        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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         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-GH-A9DA 
        0.82         3.52         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41         7.13        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       195.85        30.31         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        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        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       13.35        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         5.88         6.25        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       29.03        20.22        14.07        19.96        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       46.03        23.28        11.51        49.55        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.18               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             73.18             195.85 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             26.27              15.73 
[1] "1.2 - 73.2 (26.3)"  "0.0 - 195.8 (15.7)"
[1] "hr=" "1.6"
D22V2, continuous
                    vv
clus                  T1  T2 T3+T4
  11Q GAIN MUTATED     3   1     1
  11Q GAIN WILD-TYPE 118  49    10
D22V3, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   3                118
  T2                   1                 49
  T3+T4                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   3
  11Q GAIN WILD-TYPE 108  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    3
  11Q GAIN WILD-TYPE  108   44
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                108
  1                3                 44
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11Q GAIN MUTATED    3  1  2
  11Q GAIN WILD-TYPE 88  7 91
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                3                 88
  M1                1                  7
  MX                2                 91
[1] 3 2
[1] 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                                5
  11Q GAIN WILD-TYPE             5                              192
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11Q GAIN MUTATED                                               0
  11Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11Q GAIN MUTATED                                     2
  11Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11Q GAIN MUTATED                                           0
  11Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11Q GAIN MUTATED                                              0
  11Q GAIN WILD-TYPE                                            6
D22V6, multiclass
                                               clus
vv                                              11Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             5
  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                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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   5
  11Q GAIN WILD-TYPE  28 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    5
  11Q GAIN WILD-TYPE   28  203
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 2                 28
  YES                5                203
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 72 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         TCGA-HM-A4S6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-AAVH         TCGA-JX-A3Q0         TCGA-MU-A5YI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PG         TCGA-VS-A8EH         TCGA-VS-A8QM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A94Y         TCGA-VS-A94Z         TCGA-WL-A834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED                           1
  11Q GAIN WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           0     5
  11Q GAIN WILD-TYPE                                         1   164
D22V10, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 18
  BLACK OR AFRICAN AMERICAN                                1                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                164
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1   4
  11Q GAIN WILD-TYPE  15 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    4
  11Q GAIN WILD-TYPE   15  145
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO                4                145
[1] 2 2
[1] FALSE
D22V12, continuous
D22V13, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  1
  11Q GAIN WILD-TYPE 69 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    1
  11Q GAIN WILD-TYPE   69   24
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  TUMOR FREE                2                 69
  WITH TUMOR                1                 24
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  11Q GAIN MUTATED        0      1       0      0       0             6       0
  11Q GAIN WILD-TYPE     23      4       1     10       7           172      14
D22V14, multiclass
               clus
vv              11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  BRAZIL                       0                 23
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  7
  UNITED STATES                6                172
  VIETNAM                      0                 14
[1] 7 2
[1] 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   7   0   0
  11Q GAIN WILD-TYPE  17 106  90   1  14
D22V15, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  G1                0                 17
  G2                0                106
  G3                7                 90
  G4                0                  1
  GX                0                 14
[1] 5 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                 72 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         TCGA-HM-A4S6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-AAVH         TCGA-JX-A3Q0         TCGA-MU-A5YI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PG         TCGA-VS-A8EH         TCGA-VS-A8QM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A94Y         TCGA-VS-A94Z         TCGA-WL-A834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11Q GAIN MUTATED                                             0
  11Q GAIN WILD-TYPE                                          31
                    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                                                 1
  11Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11Q GAIN MUTATED                1                   2
  11Q GAIN WILD-TYPE             51                 110
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                1
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                            2
                                                 clus
vv                                                11Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  51
  LIFELONG NON-SMOKER                                            110
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V19, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 66 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A8XI         TCGA-C5-A8YQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8YT         TCGA-C5-A8ZZ         TCGA-C5-A907 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EK-A2RA         TCGA-EX-A1H5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3TX         TCGA-FU-A3WB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A4S6         TCGA-HM-A6W2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VK         TCGA-JW-AAVH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-MU-A5YI         TCGA-MU-A8JM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73Q         TCGA-Q1-A73S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8EH         TCGA-VS-A8QF         TCGA-VS-A8QM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A94Y         TCGA-VS-A94Z         TCGA-WL-A834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  11Q GAIN MUTATED             0        1             2        1
  11Q GAIN WILD-TYPE          19       74            10       11
D22V21, multiclass
               clus
vv              11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COMBINATION                  0                 19
  EXTERNAL                     1                 74
  EXTERNAL BEAM                2                 10
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V22, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  0
  11Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    0
  11Q GAIN WILD-TYPE   23    3
                         clus
vv                        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   2                 23
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  11Q GAIN MUTATED                    0                0                   1
  11Q GAIN WILD-TYPE                  2                2                  27
                    vv
clus                 REGIONAL SITE
  11Q GAIN MUTATED               0
  11Q GAIN WILD-TYPE            16
D22V23, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 47 
        TCGA-C5-A0TN         TCGA-C5-A1BF         TCGA-C5-A1BQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-C5-A7UE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-C5-A7X5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8XJ         TCGA-C5-A8XK         TCGA-C5-A8YQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8YT         TCGA-C5-A8ZZ         TCGA-C5-A907 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DG-A2KL         TCGA-DS-A7WF         TCGA-EX-A3L1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-HM-A3JJ         TCGA-HM-A4S6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-JW-A5VG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-R2-A69V         TCGA-UC-A7PG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8EC         TCGA-VS-A8EG         TCGA-VS-A8EH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8EI         TCGA-VS-A8EL         TCGA-VS-A8Q8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8Q9         TCGA-VS-A8QC         TCGA-VS-A8QF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8QH         TCGA-VS-A94X         TCGA-VS-A94Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A954         TCGA-VS-A957         TCGA-VS-A958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A959         TCGA-VS-A9U5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V24, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    0  1
  11Q GAIN WILD-TYPE 34  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    1
  11Q GAIN WILD-TYPE   34    2
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CGY                0                 34
  GY                 1                  2
[1] 2 2
[1] FALSE
D22V25, continuous
D22V26, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                101 
        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-A1ML 
"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-A7X3         TCGA-C5-A7X8         TCGA-C5-A8ZZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DG-A2KL         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-A5VH         TCGA-JW-A5VI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-JX-A3PZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PG         TCGA-UC-A7PI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V27, continuous
D22V28, continuous
D22V29, continuous
D22V30, 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-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-A1ML 
"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-A7X3         TCGA-C5-A7X8         TCGA-C5-A8ZZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DG-A2KL         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-A5VH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VJ         TCGA-JW-A5VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VL         TCGA-JW-A69B         TCGA-JW-A852 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3PZ         TCGA-JX-A3Q0         TCGA-JX-A3Q8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-Q1-A73Q         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF         TCGA-UC-A7PG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PI 
"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                         2                       0
  11Q GAIN WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11Q GAIN MUTATED                         0
  11Q GAIN WILD-TYPE                       7
D22V31, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 43 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1M5         TCGA-C5-A1M7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MJ         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-A2M1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HL         TCGA-C5-A7CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7UC         TCGA-C5-A7X8         TCGA-C5-A7XC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8XH         TCGA-C5-A8XI         TCGA-DG-A2KL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8QA 
"11Q GAIN WILD-TYPE" 
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  11Q GAIN MUTATED                                               0
  11Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11Q GAIN MUTATED                                                0
  11Q GAIN WILD-TYPE                                             16
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11Q GAIN MUTATED                                                                                   0
  11Q GAIN WILD-TYPE                                                                                68
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11Q GAIN MUTATED                                                                                              5
  11Q GAIN WILD-TYPE                                                                                          100
D22V32, multiclass
                                                                                              clus
vv                                                                                             11Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           0
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                5
                                                                                              clus
vv                                                                                             11Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V33, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  3
  11Q GAIN WILD-TYPE 66 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    3
  11Q GAIN WILD-TYPE   66   67
         clus
vv        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ABSENT                 2                 66
  PRESENT                3                 67
[1] 2 2
[1] FALSE
D22V34, continuous
D22V35, continuous
D22V36, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  3
  11Q GAIN WILD-TYPE 42 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    3
  11Q GAIN WILD-TYPE   42   91
                                          clus
vv                                         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                3                 91
[1] 2 2
[1] FALSE
D22V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11Q GAIN MUTATED              1           1          0
  11Q GAIN WILD-TYPE            9          48         57
D22V38, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                114 
        TCGA-C5-A1BI         TCGA-C5-A1BL         TCGA-C5-A1BN 
"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-A1MN 
"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-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7UH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-C5-A8YT         TCGA-DG-A2KM 
"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-A3LQ         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-A410         TCGA-EA-A411         TCGA-EA-A43B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A50E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EA-A5ZE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A5ZF         TCGA-EA-A97N         TCGA-EK-A2R7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EK-A3GK         TCGA-EX-A1H5         TCGA-EX-A1H6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-EX-A69L         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-A3WB         TCGA-FU-A3YQ         TCGA-FU-A57G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-HG-A9SC         TCGA-HM-A3JJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-HM-A6W2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LA         TCGA-IR-A3LB 
"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-JW-A5VG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VJ         TCGA-JW-A5VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JX-A3PZ         TCGA-JX-A3Q0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-JX-A5QV         TCGA-LP-A5U2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-LP-A5U3         TCGA-LP-A7HU         TCGA-PN-A8MA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A5R1         TCGA-Q1-A5R2         TCGA-Q1-A5R3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DV         TCGA-Q1-A73P         TCGA-Q1-A73S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PI         TCGA-VS-A8EB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8EC         TCGA-VS-A8EG         TCGA-VS-A8EH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8EI         TCGA-VS-A8EL         TCGA-VS-A8Q8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A94Y         TCGA-VS-A94Z         TCGA-VS-A952 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A954         TCGA-VS-A957         TCGA-VS-A958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A959         TCGA-VS-A9U5         TCGA-WL-A834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V39, continuous
D22V40, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4  0
  11Q GAIN WILD-TYPE 85 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    0
  11Q GAIN WILD-TYPE   85   16
         clus
vv        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ABSENT                 4                 85
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D22V41, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A3JK         TCGA-JW-A852 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-MU-A51Y         TCGA-MU-A8JM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  11Q GAIN MUTATED     0    0   2    0    1  0   0    1    0   0  0   1  0   1
  11Q GAIN WILD-TYPE   1    1  28   65   23  4   8    6    9  22  1   7  2   0
                    vv
clus                 TX
  11Q GAIN MUTATED    0
  11Q GAIN WILD-TYPE 14
D22V42, multiclass
      clus
vv     11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 2                 28
  T1B1                0                 65
  T1B2                1                 23
  T2                  0                  4
  T2A                 0                  8
  T2A1                1                  6
  T2A2                0                  9
  T2B                 0                 22
  T3                  0                  1
  T3B                 1                  7
  T4                  0                  2
  TIS                 1                  0
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  11Q GAIN MUTATED         0        0         0         0        1         1
  11Q GAIN WILD-TYPE       4        2         1         1       30        68
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  11Q GAIN MUTATED           2        0         1          0          0
  11Q GAIN WILD-TYPE        30        3         5          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  11Q GAIN MUTATED           0         0          2         0         0
  11Q GAIN WILD-TYPE        27         1         32         3         7
D22V44, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  1                 30
  STAGE IB1                 1                 68
  STAGE IB2                 2                 30
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 0                 27
  STAGE III                 0                  1
  STAGE IIIB                2                 32
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    32  12
  12P GAIN WILD-TYPE 151  38
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                44                189 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                12                 38 
$`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       154.32 
TCGA-C5-A7CK TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-DG-A2KL 
      134.33         9.34        13.61         8.35        23.51        44.94 
TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
       22.98         0.76        14.50        13.91        14.96         0.36 
TCGA-EK-A2R8 TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A5XV 
        1.45        23.84         2.17         1.45         1.48         1.97 
TCGA-GH-A9DA TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MU-A8JM TCGA-MY-A5BD 
        9.01         7.99         0.30         0.20         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EJ 
        0.07         5.49        12.16        10.03        34.52        19.96 
TCGA-VS-A94X TCGA-VS-A9U5 
       16.64        38.96 

$`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-A1ML 
       67.46        46.32        30.21        35.01         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ 
       40.93         3.58        44.22        73.45        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
       38.43         0.82        52.01        17.85        20.42       101.82 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
       94.95         2.73        50.99        45.83        75.78        99.91 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52         6.12        20.91         4.47         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       50.76        40.04        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        17.52         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-A43B TCGA-EA-A44S 
        1.18        14.50         1.35         1.35         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        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA 
        1.51         0.43         0.59         0.59         0.13        16.08 
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        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
        4.73         1.22         0.92         0.66         1.02         1.58 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.35         1.32         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        7.13        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       26.56        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        10.06         5.13         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
      195.85        30.31        11.28         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       13.87         0.03         4.34         2.96        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL 
       93.99        61.28        29.03        20.22        14.07        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        23.28        11.51        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       31.27         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            182.93             195.85 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             14.73              15.95 
[1] "0.1 - 182.9 (14.7)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.4"
D23V2, continuous
                    vv
clus                  T1  T2 T3+T4
  12P GAIN MUTATED    21  11     4
  12P GAIN WILD-TYPE 100  39     7
D23V3, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                  21                100
  T2                  11                 39
  T3+T4                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   23  8
  12P GAIN WILD-TYPE 88 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     23    8
  12P GAIN WILD-TYPE   88   39
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               23                 88
  1                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED   17  3 17
  12P GAIN WILD-TYPE 74  5 76
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               17                 74
  M1                3                  5
  MX               17                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED               0                               39
  12P GAIN WILD-TYPE             5                              158
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12P GAIN MUTATED                                               1
  12P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12P GAIN MUTATED                                     4
  12P GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12P GAIN MUTATED                                           0
  12P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12P GAIN MUTATED                                              0
  12P GAIN WILD-TYPE                                            6
D23V6, multiclass
                                               clus
vv                                              12P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            39
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              12P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             158
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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  37
  12P GAIN WILD-TYPE  23 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7   37
  12P GAIN WILD-TYPE   23  171
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 7                 23
  YES               37                171
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     4
  12P GAIN WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED                           5
  12P GAIN WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           0    32
  12P GAIN WILD-TYPE                                         1   137
D23V10, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                5                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   32                137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2  28
  12P GAIN WILD-TYPE  14 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   28
  12P GAIN WILD-TYPE   14  121
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               28                121
[1] 2 2
[1] FALSE
D23V12, continuous
D23V13, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   12  4
  12P GAIN WILD-TYPE 59 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     12    4
  12P GAIN WILD-TYPE   59   21
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  TUMOR FREE               12                 59
  WITH TUMOR                4                 21
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  12P GAIN MUTATED        5      1       0      1       2            31       4
  12P GAIN WILD-TYPE     18      4       1      9       5           147      10
D23V14, multiclass
               clus
vv              12P GAIN MUTATED 12P GAIN WILD-TYPE
  BRAZIL                       5                 18
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      2                  5
  UNITED STATES               31                147
  VIETNAM                      4                 10
[1] 7 2
[1] 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    4 18 21  0  1
  12P GAIN WILD-TYPE 13 88 76  1 13
D23V15, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  G1                4                 13
  G2               18                 88
  G3               21                 76
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V16, continuous
D23V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12P GAIN MUTATED                                             4
  12P GAIN WILD-TYPE                                          27
                    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                                                 2
  12P GAIN WILD-TYPE                                               0
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12P GAIN MUTATED               13                  20
  12P GAIN WILD-TYPE             39                  92
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                2
  CURRENT SMOKER                                                13
  LIFELONG NON-SMOKER                                           20
                                                 clus
vv                                                12P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  0
  CURRENT SMOKER                                                  39
  LIFELONG NON-SMOKER                                             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"
D23V19, continuous
D23V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  12P GAIN MUTATED             5       14             2        3
  12P GAIN WILD-TYPE          14       61            10        9
D23V21, multiclass
               clus
vv              12P GAIN MUTATED 12P GAIN WILD-TYPE
  COMBINATION                  5                 14
  EXTERNAL                    14                 61
  EXTERNAL BEAM                2                 10
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V22, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    7  0
  12P GAIN WILD-TYPE 18  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    0
  12P GAIN WILD-TYPE   18    3
                         clus
vv                        12P GAIN MUTATED 12P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   7                 18
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  12P GAIN MUTATED                    0                0                  10
  12P GAIN WILD-TYPE                  2                2                  18
                    vv
clus                 REGIONAL SITE
  12P GAIN MUTATED               2
  12P GAIN WILD-TYPE            14
D23V23, multiclass
                     clus
vv                    12P GAIN MUTATED 12P GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD               10                 18
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V24, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    8  1
  12P GAIN WILD-TYPE 26  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8    1
  12P GAIN WILD-TYPE   26    2
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  CGY                8                 26
  GY                 1                  2
[1] 2 2
[1] FALSE
D23V25, continuous
D23V26, continuous
D23V27, continuous
D23V28, continuous
D23V29, continuous
D23V30, 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                         7                       0
  12P GAIN WILD-TYPE                      22                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12P GAIN MUTATED                         3
  12P GAIN WILD-TYPE                       4
D23V31, multiclass
                                     clus
vv                                    12P GAIN MUTATED 12P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            7                 22
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  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)
  12P GAIN MUTATED                                               0
  12P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12P GAIN MUTATED                                                4
  12P GAIN WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12P GAIN MUTATED                                                                                  15
  12P GAIN WILD-TYPE                                                                                53
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12P GAIN MUTATED                                                                                             16
  12P GAIN WILD-TYPE                                                                                           89
D23V32, multiclass
                                                                                              clus
vv                                                                                             12P 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)                          15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               16
                                                                                              clus
vv                                                                                             12P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V33, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   15 12
  12P GAIN WILD-TYPE 53 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     15   12
  12P GAIN WILD-TYPE   53   58
         clus
vv        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ABSENT                15                 53
  PRESENT               12                 58
[1] 2 2
[1] FALSE
D23V34, continuous
D23V35, continuous
D23V36, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   13 14
  12P GAIN WILD-TYPE 30 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13   14
  12P GAIN WILD-TYPE   30   80
                                          clus
vv                                         12P GAIN MUTATED 12P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   13                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               14                 80
[1] 2 2
[1] FALSE
D23V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12P GAIN MUTATED              1           8         10
  12P GAIN WILD-TYPE            9          41         47
D23V38, multiclass
              clus
vv             12P GAIN MUTATED 12P GAIN WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 8                 41
  NEVER USED                 10                 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"
D23V39, continuous
D23V40, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   17  3
  12P GAIN WILD-TYPE 72 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     17    3
  12P GAIN WILD-TYPE   72   13
         clus
vv        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ABSENT                17                 72
  PRESENT                3                 13
[1] 2 2
[1] FALSE
D23V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  12P GAIN MUTATED     0    0   4    9    8  2   2    2    0   5  0   4  0   1
  12P GAIN WILD-TYPE   1    1  26   56   16  2   6    5    9  17  1   4  2   0
                    vv
clus                 TX
  12P GAIN MUTATED    0
  12P GAIN WILD-TYPE 14
D23V42, multiclass
      clus
vv     12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 4                 26
  T1B1                9                 56
  T1B2                8                 16
  T2                  2                  2
  T2A                 2                  6
  T2A1                2                  5
  T2A2                0                  9
  T2B                 5                 17
  T3                  0                  1
  T3B                 4                  4
  T4                  0                  2
  TIS                 1                  0
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  12P GAIN MUTATED         0        0         0         0        3        12
  12P GAIN WILD-TYPE       4        2         1         1       28        57
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  12P GAIN MUTATED           7        1         2          2          0
  12P GAIN WILD-TYPE        25        2         4          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  12P GAIN MUTATED           7         0          8         1         1
  12P GAIN WILD-TYPE        20         1         26         2         6
D23V44, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 28
  STAGE IB1                12                 57
  STAGE IB2                 7                 25
  STAGE II                  1                  2
  STAGE IIA                 2                  4
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                 7                 20
  STAGE III                 0                  1
  STAGE IIIB                8                 26
  STAGE IVA                 1                  2
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    31  10
  12Q GAIN WILD-TYPE 152  40
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                41                192 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                10                 40 
$`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-C5-A8XH TCGA-C5-A8XI TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ 
        9.34        45.83         8.35        58.88        44.94        22.98 
TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2R8 TCGA-FU-A23L 
        0.76        14.50        14.96         0.36         1.45        23.84 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A5XV TCGA-GH-A9DA TCGA-JX-A5QV TCGA-LP-A5U2 
        1.45         1.48         1.97         9.01         7.99         0.30 
TCGA-LP-A7HU TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A5R3 
        0.20         5.42        29.72         0.07         5.49        15.95 
TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A9U5 
       12.16        34.52        19.96        16.64        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY 
       20.91        40.93         3.58        44.22        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
      100.14        38.43         0.82        17.85        20.42       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82        15.48        20.35       147.35        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XJ 
       60.69        94.95        13.61         2.73        50.99        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        50.76        40.04        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        17.52 
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 
       15.02        14.99        13.58        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         6.12         4.73         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-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.12        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       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        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
        5.13         6.71        21.11       195.85        30.31        11.28 
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        15.58        13.35         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
        3.88        11.67        93.99        61.28        10.03        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       20.22        14.07        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z 
       11.51        49.55        39.78        31.27         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       44.88        42.58        42.08        43.82        39.35        18.05 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            182.93             195.85 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             16.64              15.58 
[1] "0.1 - 182.9 (16.6)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                  T1  T2 T3+T4
  12Q GAIN MUTATED    21  10     3
  12Q GAIN WILD-TYPE 100  40     8
D24V3, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                  21                100
  T2                  10                 40
  T3+T4                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   21  9
  12Q GAIN WILD-TYPE 90 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     21    9
  12Q GAIN WILD-TYPE   90   38
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               21                 90
  1                9                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED   16  2 18
  12Q GAIN WILD-TYPE 75  6 75
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               16                 75
  M1                2                  6
  MX               18                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED               0                               38
  12Q GAIN WILD-TYPE             5                              159
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12Q GAIN MUTATED                                               1
  12Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12Q GAIN MUTATED                                     2
  12Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12Q GAIN MUTATED                                           0
  12Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12Q GAIN MUTATED                                              0
  12Q GAIN WILD-TYPE                                            6
D24V6, multiclass
                                               clus
vv                                              12Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              12Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             159
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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     8  33
  12Q GAIN WILD-TYPE  22 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8   33
  12Q GAIN WILD-TYPE   22  175
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 8                 22
  YES               33                175
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     4
  12Q GAIN WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED                           4
  12Q GAIN WILD-TYPE                        20
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           0    29
  12Q GAIN WILD-TYPE                                         1   140
D24V10, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                4                 20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   29                140
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  25
  12Q GAIN WILD-TYPE  14 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   25
  12Q GAIN WILD-TYPE   14  124
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               25                124
[1] 2 2
[1] FALSE
D24V12, continuous
D24V13, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12  4
  12Q GAIN WILD-TYPE 59 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12    4
  12Q GAIN WILD-TYPE   59   21
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  TUMOR FREE               12                 59
  WITH TUMOR                4                 21
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  12Q GAIN MUTATED        4      2       0      1       1            29       4
  12Q GAIN WILD-TYPE     19      3       1      9       6           149      10
D24V14, multiclass
               clus
vv              12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  BRAZIL                       4                 19
  CANADA                       2                  3
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      1                  6
  UNITED STATES               29                149
  VIETNAM                      4                 10
[1] 7 2
[1] 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    3 16 21  0  0
  12Q GAIN WILD-TYPE 14 90 76  1 14
D24V15, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  G1                3                 14
  G2               16                 90
  G3               21                 76
  G4                0                  1
  GX                0                 14
[1] 5 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                                             5
  12Q GAIN WILD-TYPE                                          26
                    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                                                 2
  12Q GAIN WILD-TYPE                                               0
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12Q GAIN MUTATED               10                  19
  12Q GAIN WILD-TYPE             42                  93
D24V18, multiclass
                                                 clus
vv                                                12Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                10
  LIFELONG NON-SMOKER                                           19
                                                 clus
vv                                                12Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  0
  CURRENT SMOKER                                                  42
  LIFELONG NON-SMOKER                                             93
[1] 5 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
D24V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  12Q GAIN MUTATED             6       12             2        3
  12Q GAIN WILD-TYPE          13       63            10        9
D24V21, multiclass
               clus
vv              12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COMBINATION                  6                 13
  EXTERNAL                    12                 63
  EXTERNAL BEAM                2                 10
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V22, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8  0
  12Q GAIN WILD-TYPE 17  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8    0
  12Q GAIN WILD-TYPE   17    3
                         clus
vv                        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   8                 17
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  12Q GAIN MUTATED                    0                0                   8
  12Q GAIN WILD-TYPE                  2                2                  20
                    vv
clus                 REGIONAL SITE
  12Q GAIN MUTATED               2
  12Q GAIN WILD-TYPE            14
D24V23, multiclass
                     clus
vv                    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                8                 20
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V24, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    7  1
  12Q GAIN WILD-TYPE 27  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7    1
  12Q GAIN WILD-TYPE   27    2
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CGY                7                 27
  GY                 1                  2
[1] 2 2
[1] FALSE
D24V25, continuous
D24V26, continuous
D24V27, continuous
D24V28, continuous
D24V29, continuous
D24V30, 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                         7                       0
  12Q GAIN WILD-TYPE                      22                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12Q GAIN MUTATED                         2
  12Q GAIN WILD-TYPE                       5
D24V31, multiclass
                                     clus
vv                                    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            7                 22
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  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)
  12Q GAIN MUTATED                                               0
  12Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12Q GAIN MUTATED                                                4
  12Q GAIN WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12Q GAIN MUTATED                                                                                  14
  12Q GAIN WILD-TYPE                                                                                54
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12Q GAIN MUTATED                                                                                             13
  12Q GAIN WILD-TYPE                                                                                           92
D24V32, multiclass
                                                                                              clus
vv                                                                                             12Q 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)                          14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               13
                                                                                              clus
vv                                                                                             12Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V33, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12 12
  12Q GAIN WILD-TYPE 56 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12   12
  12Q GAIN WILD-TYPE   56   58
         clus
vv        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ABSENT                12                 56
  PRESENT               12                 58
[1] 2 2
[1] FALSE
D24V34, continuous
D24V35, continuous
D24V36, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12 15
  12Q GAIN WILD-TYPE 31 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12   15
  12Q GAIN WILD-TYPE   31   79
                                          clus
vv                                         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   12                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               15                 79
[1] 2 2
[1] FALSE
D24V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12Q GAIN MUTATED              1           8          8
  12Q GAIN WILD-TYPE            9          41         49
D24V38, multiclass
              clus
vv             12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 8                 41
  NEVER USED                  8                 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"
D24V39, continuous
D24V40, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   15  3
  12Q GAIN WILD-TYPE 74 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     15    3
  12Q GAIN WILD-TYPE   74   13
         clus
vv        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ABSENT                15                 74
  PRESENT                3                 13
[1] 2 2
[1] FALSE
D24V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  12Q GAIN MUTATED     0    0   5    9    7  2   2    2    0   4  0   3  0   1
  12Q GAIN WILD-TYPE   1    1  25   56   17  2   6    5    9  18  1   5  2   0
                    vv
clus                 TX
  12Q GAIN MUTATED    1
  12Q GAIN WILD-TYPE 13
D24V42, multiclass
      clus
vv     12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 5                 25
  T1B1                9                 56
  T1B2                7                 17
  T2                  2                  2
  T2A                 2                  6
  T2A1                2                  5
  T2A2                0                  9
  T2B                 4                 18
  T3                  0                  1
  T3B                 3                  5
  T4                  0                  2
  TIS                 1                  0
  TX                  1                 13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  12Q GAIN MUTATED         0        0         0         0        3        11
  12Q GAIN WILD-TYPE       4        2         1         1       28        58
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  12Q GAIN MUTATED           6        1         2          2          0
  12Q GAIN WILD-TYPE        26        2         4          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  12Q GAIN MUTATED           6         0          8         1         0
  12Q GAIN WILD-TYPE        21         1         26         2         7
D24V44, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 28
  STAGE IB1                11                 58
  STAGE IB2                 6                 26
  STAGE II                  1                  2
  STAGE IIA                 2                  4
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                 6                 21
  STAGE III                 0                  1
  STAGE IIIB                8                 26
  STAGE IVA                 1                  2
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    14   7
  13Q GAIN WILD-TYPE 169  43
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                212 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                 43 
$`13Q GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7X8 TCGA-C5-A8YR 
       35.01         0.46       100.14        17.85         2.73        27.52 
TCGA-DG-A2KH TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
        1.12         0.62        13.05        13.91        14.96         0.36 
TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EX-A8YF TCGA-FU-A40J TCGA-MY-A5BE TCGA-PN-A8MA 
        1.51         1.18         4.73         1.35         0.07         2.96 
TCGA-Q1-A73R TCGA-VS-A8Q8 TCGA-VS-A8QH 
        6.25        32.15        39.78 

$`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-A1ML TCGA-C5-A1MN 
       53.16        38.99        35.61         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43         0.82        52.01        18.02        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19        85.55        60.69        94.95         9.34        13.61 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       50.99        45.83         8.35        75.78        99.91        23.51 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
        6.12        20.91         4.47        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        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        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QE 
        0.76        12.36         1.74         1.32         0.82         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        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
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-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70        19.79         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       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        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        5.13         6.71        21.11       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89         0.07         0.30         0.82         0.20 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       13.87         0.03         5.42        29.72         4.34         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88         5.88        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 
       29.03        20.22        14.07        19.96        53.52        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        11.51        49.55        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.07               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            100.14             195.85 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              4.73              16.41 
[1] "0.1 - 100.1 (4.7)"  "0.0 - 195.8 (16.4)"
[1] "hr=" "3"  
D25V2, continuous
                    vv
clus                  T1  T2 T3+T4
  13Q GAIN MUTATED    11   4     1
  13Q GAIN WILD-TYPE 110  46    10
D25V3, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                  11                110
  T2                   4                 46
  T3+T4                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    11   4
  13Q GAIN WILD-TYPE 100  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     11    4
  13Q GAIN WILD-TYPE  100   43
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               11                100
  1                4                 43
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  13Q GAIN MUTATED   11  0  7
  13Q GAIN WILD-TYPE 80  8 86
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               11                 80
  M1                0                  8
  MX                7                 86
[1] 3 2
[1] 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               1                               13
  13Q GAIN WILD-TYPE             4                              184
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  13Q GAIN MUTATED                                               0
  13Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  13Q GAIN MUTATED                                     4
  13Q GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  13Q GAIN MUTATED                                           0
  13Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  13Q GAIN MUTATED                                              3
  13Q GAIN WILD-TYPE                                            3
D25V6, multiclass
                                               clus
vv                                              13Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            13
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 3
                                               clus
vv                                              13Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             184
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  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"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     2  19
  13Q GAIN WILD-TYPE  28 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   19
  13Q GAIN WILD-TYPE   28  189
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 2                 28
  YES               19                189
[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                                8    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED                           3
  13Q GAIN WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           0    16
  13Q GAIN WILD-TYPE                                         1   153
D25V10, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                3                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                153
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  14
  13Q GAIN WILD-TYPE  16 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   14
  13Q GAIN WILD-TYPE   16  135
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               14                135
[1] 2 2
[1] FALSE
D25V12, continuous
D25V13, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  4
  13Q GAIN WILD-TYPE 68 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    4
  13Q GAIN WILD-TYPE   68   21
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  TUMOR FREE                3                 68
  WITH TUMOR                4                 21
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  13Q GAIN MUTATED        2      1       1      1       2            13       1
  13Q GAIN WILD-TYPE     21      4       0      9       5           165      13
D25V14, multiclass
               clus
vv              13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  BRAZIL                       2                 21
  CANADA                       1                  4
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      2                  5
  UNITED STATES               13                165
  VIETNAM                      1                 13
[1] 7 2
[1] 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  9  9  0  2
  13Q GAIN WILD-TYPE 16 97 88  1 12
D25V15, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  G1                1                 16
  G2                9                 97
  G3                9                 88
  G4                0                  1
  GX                2                 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"
D25V16, continuous
D25V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  13Q GAIN MUTATED                                             1
  13Q GAIN WILD-TYPE                                          30
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  13Q GAIN MUTATED                3                  14
  13Q GAIN WILD-TYPE             49                  98
D25V18, multiclass
                                                 clus
vv                                                13Q 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                                                 3
  LIFELONG NON-SMOKER                                           14
                                                 clus
vv                                                13Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  49
  LIFELONG NON-SMOKER                                             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"
D25V19, continuous
D25V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  13Q GAIN MUTATED             1        8             1        0
  13Q GAIN WILD-TYPE          18       67            11       12
D25V21, multiclass
               clus
vv              13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COMBINATION                  1                 18
  EXTERNAL                     8                 67
  EXTERNAL BEAM                1                 11
  INTERNAL                     0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V22, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  0
  13Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    0
  13Q GAIN WILD-TYPE   23    3
                         clus
vv                        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   2                 23
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  13Q GAIN MUTATED                    0                0                   2
  13Q GAIN WILD-TYPE                  2                2                  26
                    vv
clus                 REGIONAL SITE
  13Q GAIN MUTATED               1
  13Q GAIN WILD-TYPE            15
D25V23, multiclass
                     clus
vv                    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                2                 26
  REGIONAL SITE                      1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V24, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  0
  13Q GAIN WILD-TYPE 32  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    0
  13Q GAIN WILD-TYPE   32    3
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CGY                2                 32
  GY                 0                  3
[1] 2 2
[1] FALSE
D25V25, continuous
D25V26, continuous
D25V27, continuous
D25V28, continuous
D25V29, continuous
D25V30, 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                         3                       0
  13Q GAIN WILD-TYPE                      26                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  13Q GAIN MUTATED                         0
  13Q GAIN WILD-TYPE                       7
D25V31, multiclass
                                     clus
vv                                    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            3                 26
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  13Q GAIN MUTATED                                                                                   7
  13Q GAIN WILD-TYPE                                                                                61
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  13Q GAIN MUTATED                                                                                             10
  13Q GAIN WILD-TYPE                                                                                           95
D25V32, 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)                           7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               10
                                                                                              clus
vv                                                                                             13Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V33, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    7  7
  13Q GAIN WILD-TYPE 61 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7    7
  13Q GAIN WILD-TYPE   61   63
         clus
vv        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ABSENT                 7                 61
  PRESENT                7                 63
[1] 2 2
[1] FALSE
D25V34, continuous
D25V35, continuous
D25V36, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  8
  13Q GAIN WILD-TYPE 41 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    8
  13Q GAIN WILD-TYPE   41   86
                                          clus
vv                                         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    2                 41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                8                 86
[1] 2 2
[1] FALSE
D25V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  13Q GAIN MUTATED              0           5          3
  13Q GAIN WILD-TYPE           10          44         54
D25V38, multiclass
              clus
vv             13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 5                 44
  NEVER USED                  3                 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"
D25V39, continuous
D25V40, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    8  0
  13Q GAIN WILD-TYPE 81 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      8    0
  13Q GAIN WILD-TYPE   81   16
         clus
vv        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ABSENT                 8                 81
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D25V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  13Q GAIN MUTATED     0    0   3    5    3  0   1    2    0   1  0   1  0   0
  13Q GAIN WILD-TYPE   1    1  27   60   21  4   7    5    9  21  1   7  2   1
                    vv
clus                 TX
  13Q GAIN MUTATED    2
  13Q GAIN WILD-TYPE 12
D25V42, multiclass
      clus
vv     13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 3                 27
  T1B1                5                 60
  T1B2                3                 21
  T2                  0                  4
  T2A                 1                  7
  T2A1                2                  5
  T2A2                0                  9
  T2B                 1                 21
  T3                  0                  1
  T3B                 1                  7
  T4                  0                  2
  TIS                 0                  1
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  13Q GAIN MUTATED         1        0         0         0        3         8
  13Q GAIN WILD-TYPE       3        2         1         1       28        61
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  13Q GAIN MUTATED           4        0         0          0          0
  13Q GAIN WILD-TYPE        28        3         6          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  13Q GAIN MUTATED           1         0          3         0         0
  13Q GAIN WILD-TYPE        26         1         31         3         7
D25V44, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 28
  STAGE IB1                 8                 61
  STAGE IB2                 4                 28
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 1                 26
  STAGE III                 0                  1
  STAGE IIIB                3                 31
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    27   7
  14Q GAIN WILD-TYPE 156  43
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                34                199 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                 43 
$`14Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BL TCGA-C5-A1M6 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A2LT 
       57.04       173.29        31.40        38.99        35.61        73.18 
TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-DS-A7WI TCGA-EA-A1QS 
       73.45       154.32         2.73        45.83         8.28         0.76 
TCGA-EA-A3QE TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
        1.18        14.50        14.89        13.91        14.96         0.36 
TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EX-A3L1 TCGA-FU-A3HY TCGA-FU-A3NI TCGA-JW-A69B 
        6.64         0.59         6.94         0.66         1.45        10.06 
TCGA-JX-A3Q8 TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MY-A5BD TCGA-MY-A913 TCGA-Q1-A6DT 
       30.31         0.30         0.82        29.72         5.49         3.39 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A9U5 
       20.22        14.07        19.96        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX 
        2.43        20.91        40.93         3.58        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43         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 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34        13.61        50.99         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       58.88        50.76        44.94        40.04        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-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52        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-A43B 
        0.62        13.05        14.50         1.35         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.66        12.82         0.26         1.48        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG 
       13.58        13.48        12.59        45.96        26.27         1.51 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.59         1.45         0.13        16.08         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-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        7.92        14.70        19.79         6.12         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
       23.84         0.92         2.17         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        20.48        15.58         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85         7.99        11.28         0.89         0.07 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF 
        0.20        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        15.58        13.35        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
        3.88        11.67        93.99        12.16        61.28        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       34.52        29.03        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-WL-A834 
       18.05 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.30               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            173.29             195.85 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            14.285             16.140 
[1] "0.3 - 173.3 (14.3)" "0.0 - 195.8 (16.1)"
[1] "hr=" "1"  
D26V2, continuous
                    vv
clus                  T1  T2 T3+T4
  14Q GAIN MUTATED    19   8     2
  14Q GAIN WILD-TYPE 102  42     9
D26V3, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                  19                102
  T2                   8                 42
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   15  9
  14Q GAIN WILD-TYPE 96 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15    9
  14Q GAIN WILD-TYPE   96   38
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               15                 96
  1                9                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  14Q GAIN MUTATED   18  2 11
  14Q GAIN WILD-TYPE 73  6 82
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               18                 73
  M1                2                  6
  MX               11                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED               0                               30
  14Q GAIN WILD-TYPE             5                              167
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  14Q GAIN MUTATED                                               1
  14Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  14Q GAIN MUTATED                                     2
  14Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  14Q GAIN MUTATED                                           1
  14Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  14Q GAIN MUTATED                                              1
  14Q GAIN WILD-TYPE                                            5
D26V6, multiclass
                                               clus
vv                                              14Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            30
  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                                              14Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             167
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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  30
  14Q GAIN WILD-TYPE  25 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   30
  14Q GAIN WILD-TYPE   25  178
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 5                 25
  YES               30                178
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     5
  14Q GAIN WILD-TYPE                                8    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED                           2
  14Q GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    27
  14Q GAIN WILD-TYPE                                         1   142
D26V10, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    5                 13
  BLACK OR AFRICAN AMERICAN                                2                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   27                142
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     3  25
  14Q GAIN WILD-TYPE  13 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3   25
  14Q GAIN WILD-TYPE   13  124
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               25                124
[1] 2 2
[1] FALSE
D26V12, continuous
D26V13, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    9  6
  14Q GAIN WILD-TYPE 62 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9    6
  14Q GAIN WILD-TYPE   62   19
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  TUMOR FREE                9                 62
  WITH TUMOR                6                 19
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  14Q GAIN MUTATED        4      0       0      3       2            22       4
  14Q GAIN WILD-TYPE     19      5       1      7       5           156      10
D26V14, multiclass
               clus
vv              14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  BRAZIL                       4                 19
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       3                  7
  UKRAINE                      2                  5
  UNITED STATES               22                156
  VIETNAM                      4                 10
[1] 7 2
[1] 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 14 16  0  3
  14Q GAIN WILD-TYPE 16 92 81  1 11
D26V15, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  G1                1                 16
  G2               14                 92
  G3               16                 81
  G4                0                  1
  GX                3                 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"
D26V16, continuous
D26V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  14Q GAIN MUTATED                                             2
  14Q GAIN WILD-TYPE                                          29
                    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                                                 1
  14Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  14Q GAIN MUTATED                9                  19
  14Q GAIN WILD-TYPE             43                  93
D26V18, multiclass
                                                 clus
vv                                                14Q GAIN 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                                                 9
  LIFELONG NON-SMOKER                                           19
                                                 clus
vv                                                14Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  43
  LIFELONG NON-SMOKER                                             93
[1] 5 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
D26V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  14Q GAIN MUTATED             4        8             1        1
  14Q GAIN WILD-TYPE          15       67            11       11
D26V21, multiclass
               clus
vv              14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COMBINATION                  4                 15
  EXTERNAL                     8                 67
  EXTERNAL BEAM                1                 11
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V22, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    5  0
  14Q GAIN WILD-TYPE 20  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5    0
  14Q GAIN WILD-TYPE   20    3
                         clus
vv                        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   5                 20
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  14Q GAIN MUTATED                    0                0                   4
  14Q GAIN WILD-TYPE                  2                2                  24
                    vv
clus                 REGIONAL SITE
  14Q GAIN MUTATED               1
  14Q GAIN WILD-TYPE            15
D26V23, multiclass
                     clus
vv                    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                4                 24
  REGIONAL SITE                      1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V24, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    4  1
  14Q GAIN WILD-TYPE 30  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    1
  14Q GAIN WILD-TYPE   30    2
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CGY                4                 30
  GY                 1                  2
[1] 2 2
[1] FALSE
D26V25, continuous
D26V26, continuous
D26V27, continuous
D26V28, continuous
D26V29, continuous
D26V30, 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                         4                       0
  14Q GAIN WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  14Q GAIN MUTATED                         0
  14Q GAIN WILD-TYPE                       7
D26V31, multiclass
                                     clus
vv                                    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            4                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  14Q GAIN MUTATED                                               0
  14Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  14Q GAIN MUTATED                                                4
  14Q GAIN WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  14Q GAIN MUTATED                                                                                   6
  14Q GAIN WILD-TYPE                                                                                62
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  14Q GAIN MUTATED                                                                                             20
  14Q GAIN WILD-TYPE                                                                                           85
D26V32, multiclass
                                                                                              clus
vv                                                                                             14Q 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)                           6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               20
                                                                                              clus
vv                                                                                             14Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V33, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   11 10
  14Q GAIN WILD-TYPE 57 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     11   10
  14Q GAIN WILD-TYPE   57   60
         clus
vv        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ABSENT                11                 57
  PRESENT               10                 60
[1] 2 2
[1] FALSE
D26V34, continuous
D26V35, continuous
D26V36, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    5 15
  14Q GAIN WILD-TYPE 38 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   15
  14Q GAIN WILD-TYPE   38   79
                                          clus
vv                                         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    5                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               15                 79
[1] 2 2
[1] FALSE
D26V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  14Q GAIN MUTATED              3           4         14
  14Q GAIN WILD-TYPE            7          45         43
D26V38, multiclass
              clus
vv             14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CURRENT USER                3                  7
  FORMER USER                 4                 45
  NEVER USED                 14                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V39, continuous
D26V40, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   14  2
  14Q GAIN WILD-TYPE 75 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14    2
  14Q GAIN WILD-TYPE   75   14
         clus
vv        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ABSENT                14                 75
  PRESENT                2                 14
[1] 2 2
[1] FALSE
D26V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  14Q GAIN MUTATED     1    0   4   10    4  0   2    2    1   3  0   2  0   1
  14Q GAIN WILD-TYPE   0    1  26   55   20  4   6    5    8  19  1   6  2   0
                    vv
clus                 TX
  14Q GAIN MUTATED    1
  14Q GAIN WILD-TYPE 13
D26V42, multiclass
      clus
vv     14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1A                 1                  0
  T1A1                0                  1
  T1B                 4                 26
  T1B1               10                 55
  T1B2                4                 20
  T2                  0                  4
  T2A                 2                  6
  T2A1                2                  5
  T2A2                1                  8
  T2B                 3                 19
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 1                  0
  TX                  1                 13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  14Q GAIN MUTATED         1        1         0         0        6         9
  14Q GAIN WILD-TYPE       3        1         1         1       25        60
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  14Q GAIN MUTATED           4        0         1          2          1
  14Q GAIN WILD-TYPE        28        3         5          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  14Q GAIN MUTATED           6         0          4         0         0
  14Q GAIN WILD-TYPE        21         1         30         3         7
D26V44, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  1                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 25
  STAGE IB1                 9                 60
  STAGE IB2                 4                 28
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                 6                 21
  STAGE III                 0                  1
  STAGE IIIB                4                 30
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    34  10
  15Q GAIN WILD-TYPE 149  40
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                44                189 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 40 
$`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-C5-A8ZZ TCGA-C5-A907 
      101.82        20.35         9.34         2.73        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KL TCGA-EA-A3HQ TCGA-EA-A5O9 TCGA-EK-A2RC TCGA-EK-A2RD 
        1.12        44.94         1.74        13.91         4.04         0.03 
TCGA-EK-A2RM TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L TCGA-HG-A9SC 
        2.24         6.94        19.79         4.73        23.84         7.13 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE 
       27.42        21.44         7.99        11.28         0.30         0.07 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EH TCGA-VS-A8EI 
       10.39        19.59        12.16        34.52        20.22        14.07 
TCGA-VS-A8QC TCGA-VS-A8QF 
       11.51        49.55 

$`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-A1ML 
       46.32        35.01        53.16        38.99         0.46        20.91 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        73.45        83.05        78.35        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK 
       52.01        17.85        20.42       182.93       154.32       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM 
       23.51        27.52         6.12        58.88        50.76        40.04 
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        17.52         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        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ 
        1.45         0.13        16.08         0.07         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-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        9.01        25.41        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        26.56        36.36         3.29        24.56        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        10.06         5.13         6.71        21.11       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       30.31         0.89         0.07         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
        0.03         5.42        29.72         4.34         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD 
       14.07        15.88         5.88         6.25         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL 
       93.99        61.28        10.03        29.03        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       32.15        46.03        23.28        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.03               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            101.82             195.85 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            16.045             15.880 
[1] "0.0 - 101.8 (16.0)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.3"
D27V2, continuous
                    vv
clus                  T1  T2 T3+T4
  15Q GAIN MUTATED    14  13     4
  15Q GAIN WILD-TYPE 107  37     7
D27V3, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                  14                107
  T2                  13                 37
  T3+T4                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   18  9
  15Q GAIN WILD-TYPE 93 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     18    9
  15Q GAIN WILD-TYPE   93   38
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               18                 93
  1                9                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  15Q GAIN MUTATED   19  0 15
  15Q GAIN WILD-TYPE 72  8 78
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               19                 72
  M1                0                  8
  MX               15                 78
[1] 3 2
[1] 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               3                               37
  15Q GAIN WILD-TYPE             2                              160
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  15Q GAIN MUTATED                                               2
  15Q GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  15Q GAIN MUTATED                                     2
  15Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  15Q GAIN MUTATED                                           0
  15Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  15Q GAIN MUTATED                                              1
  15Q GAIN WILD-TYPE                                            5
D27V6, multiclass
                                               clus
vv                                              15Q GAIN MUTATED
  ADENOSQUAMOUS                                                3
  CERVICAL SQUAMOUS CELL CARCINOMA                            37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              15Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             160
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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  38
  15Q GAIN WILD-TYPE  23 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7   38
  15Q GAIN WILD-TYPE   23  170
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 7                 23
  YES               38                170
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  3     3
  15Q GAIN WILD-TYPE                                5    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED                           2
  15Q GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           0    33
  15Q GAIN WILD-TYPE                                         1   136
D27V10, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  5
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                2                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   33                136
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     4  28
  15Q GAIN WILD-TYPE  12 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   28
  15Q GAIN WILD-TYPE   12  121
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               28                121
[1] 2 2
[1] FALSE
D27V12, continuous
D27V13, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   13  6
  15Q GAIN WILD-TYPE 58 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13    6
  15Q GAIN WILD-TYPE   58   19
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  TUMOR FREE               13                 58
  WITH TUMOR                6                 19
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  15Q GAIN MUTATED        5      2       0      1       1            34       2
  15Q GAIN WILD-TYPE     18      3       1      9       6           144      12
D27V14, multiclass
               clus
vv              15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  BRAZIL                       5                 18
  CANADA                       2                  3
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      1                  6
  UNITED STATES               34                144
  VIETNAM                      2                 12
[1] 7 2
[1] 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    4 19 20  0  2
  15Q GAIN WILD-TYPE 13 87 77  1 12
D27V15, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  G1                4                 13
  G2               19                 87
  G3               20                 77
  G4                0                  1
  GX                2                 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"
D27V16, continuous
D27V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  15Q GAIN MUTATED                                             7
  15Q GAIN WILD-TYPE                                          24
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  15Q GAIN MUTATED               12                  22
  15Q GAIN WILD-TYPE             40                  90
D27V18, multiclass
                                                 clus
vv                                                15Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                12
  LIFELONG NON-SMOKER                                           22
                                                 clus
vv                                                15Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  40
  LIFELONG NON-SMOKER                                             90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V19, continuous
D27V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  15Q GAIN MUTATED             5       21             2        2
  15Q GAIN WILD-TYPE          14       54            10       10
D27V21, multiclass
               clus
vv              15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COMBINATION                  5                 14
  EXTERNAL                    21                 54
  EXTERNAL BEAM                2                 10
  INTERNAL                     2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V22, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6  1
  15Q GAIN WILD-TYPE 19  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    1
  15Q GAIN WILD-TYPE   19    2
                         clus
vv                        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   6                 19
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  15Q GAIN MUTATED                    1                0                  12
  15Q GAIN WILD-TYPE                  1                2                  16
                    vv
clus                 REGIONAL SITE
  15Q GAIN MUTATED               5
  15Q GAIN WILD-TYPE            11
D27V23, multiclass
                     clus
vv                    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 1                  1
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD               12                 16
  REGIONAL SITE                      5                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V24, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   13  1
  15Q GAIN WILD-TYPE 21  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13    1
  15Q GAIN WILD-TYPE   21    2
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CGY               13                 21
  GY                 1                  2
[1] 2 2
[1] FALSE
D27V25, continuous
D27V26, continuous
D27V27, continuous
D27V28, continuous
D27V29, continuous
D27V30, 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                         7                       0
  15Q GAIN WILD-TYPE                      22                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  15Q GAIN MUTATED                         1
  15Q GAIN WILD-TYPE                       6
D27V31, multiclass
                                     clus
vv                                    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            7                 22
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  15Q GAIN MUTATED                                               1
  15Q GAIN WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  15Q GAIN MUTATED                                                5
  15Q GAIN WILD-TYPE                                             11
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  15Q GAIN MUTATED                                                                                  11
  15Q GAIN WILD-TYPE                                                                                57
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  15Q GAIN MUTATED                                                                                             19
  15Q GAIN WILD-TYPE                                                                                           86
D27V32, multiclass
                                                                                              clus
vv                                                                                             15Q GAIN 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)                          11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               19
                                                                                              clus
vv                                                                                             15Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V33, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   12 13
  15Q GAIN WILD-TYPE 56 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     12   13
  15Q GAIN WILD-TYPE   56   57
         clus
vv        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ABSENT                12                 56
  PRESENT               13                 57
[1] 2 2
[1] FALSE
D27V34, continuous
D27V35, continuous
D27V36, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    9 14
  15Q GAIN WILD-TYPE 34 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9   14
  15Q GAIN WILD-TYPE   34   80
                                          clus
vv                                         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               14                 80
[1] 2 2
[1] FALSE
D27V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  15Q GAIN MUTATED              2           6         11
  15Q GAIN WILD-TYPE            8          43         46
D27V38, multiclass
              clus
vv             15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                 6                 43
  NEVER USED                 11                 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"
D27V39, continuous
D27V40, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   13  3
  15Q GAIN WILD-TYPE 76 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13    3
  15Q GAIN WILD-TYPE   76   13
         clus
vv        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ABSENT                13                 76
  PRESENT                3                 13
[1] 2 2
[1] FALSE
D27V41, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 11 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-GH-A9DA         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3Q8         TCGA-MU-A51Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-MY-A913 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  15Q GAIN MUTATED     0    0   3    8    3  1   6    3    0   3  0   4  0   0
  15Q GAIN WILD-TYPE   1    1  27   57   21  3   2    4    9  19  1   4  2   1
                    vv
clus                 TX
  15Q GAIN MUTATED    3
  15Q GAIN WILD-TYPE 11
D27V42, multiclass
      clus
vv     15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 3                 27
  T1B1                8                 57
  T1B2                3                 21
  T2                  1                  3
  T2A                 6                  2
  T2A1                3                  4
  T2A2                0                  9
  T2B                 3                 19
  T3                  0                  1
  T3B                 4                  4
  T4                  0                  2
  TIS                 0                  1
  TX                  3                 11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  15Q GAIN MUTATED         0        0         0         0        4        12
  15Q GAIN WILD-TYPE       4        2         1         1       27        57
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  15Q GAIN MUTATED           5        1         4          2          0
  15Q GAIN WILD-TYPE        27        2         2          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  15Q GAIN MUTATED           6         0         10         1         0
  15Q GAIN WILD-TYPE        21         1         24         2         7
D27V44, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 27
  STAGE IB1                12                 57
  STAGE IB2                 5                 27
  STAGE II                  1                  2
  STAGE IIA                 4                  2
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                 6                 21
  STAGE III                 0                  1
  STAGE IIIB               10                 24
  STAGE IVA                 1                  2
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    26   7
  16P GAIN WILD-TYPE 157  43
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                33                200 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 43 
$`16P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A2LS 
       57.04        31.40        46.32        38.99        35.61        44.22 
TCGA-C5-A7CH TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A3LQ 
      154.32         2.73        27.52         1.12        58.88        22.98 
TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF 
        8.28         1.74        13.05        14.50        13.91        14.96 
TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EX-A69L TCGA-FU-A23L 
        0.36        26.27         0.03        23.70        19.79        23.84 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-JW-A5VJ TCGA-JX-A3Q0 TCGA-PN-A8MA TCGA-UC-A7PF 
        1.45         1.35        21.44       195.85         2.96        93.99 
TCGA-UC-A7PG TCGA-VS-A8QA TCGA-VS-A9U5 
       12.16        23.28        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV 
        2.43        20.91        40.93         3.58        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-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       75.78        99.91        23.51         6.12        20.91         4.47 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        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        17.52 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
        0.76        12.36         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-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
        0.26        14.89         1.48        15.02        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       13.48        12.59        45.96         6.64         1.51         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.59         0.59         1.45         0.13        16.08         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         6.12         4.73         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-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV 
       10.06         5.13         6.71        21.11        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89         0.07         0.30         0.82         0.20 
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-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        5.49        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59         3.88        11.67        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       29.03        20.22        14.07        19.96        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       46.03        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-WL-A834 
       39.35        18.05 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.03               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            195.85             182.93 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             22.98              15.53 
[1] "0.0 - 195.8 (23.0)" "0.0 - 182.9 (15.5)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                  T1  T2 T3+T4
  16P GAIN MUTATED    17   9     3
  16P GAIN WILD-TYPE 104  41     8
D28V3, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                  17                104
  T2                   9                 41
  T3+T4                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   15 11
  16P GAIN WILD-TYPE 96 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     15   11
  16P GAIN WILD-TYPE   96   36
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               15                 96
  1               11                 36
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED   18  0 11
  16P GAIN WILD-TYPE 73  8 82
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               18                 73
  M1                0                  8
  MX               11                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED               1                               28
  16P GAIN WILD-TYPE             4                              169
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16P GAIN MUTATED                                               1
  16P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16P GAIN MUTATED                                     2
  16P GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16P GAIN MUTATED                                           0
  16P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16P GAIN MUTATED                                              1
  16P GAIN WILD-TYPE                                            5
D28V6, multiclass
                                               clus
vv                                              16P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            28
  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                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             169
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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  29
  16P GAIN WILD-TYPE  26 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   29
  16P GAIN WILD-TYPE   26  179
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 26
  YES               29                179
[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                                6    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED                           3
  16P GAIN WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           0    20
  16P GAIN WILD-TYPE                                         1   149
D28V10, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                3                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   20                149
[1] 5 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  22
  16P GAIN WILD-TYPE  15 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   22
  16P GAIN WILD-TYPE   15  127
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               22                127
[1] 2 2
[1] FALSE
D28V12, continuous
D28V13, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    9  7
  16P GAIN WILD-TYPE 62 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    7
  16P GAIN WILD-TYPE   62   18
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  TUMOR FREE                9                 62
  WITH TUMOR                7                 18
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  16P GAIN MUTATED        2      2       1      1       2            23       2
  16P GAIN WILD-TYPE     21      3       0      9       5           155      12
D28V14, multiclass
               clus
vv              16P GAIN MUTATED 16P GAIN WILD-TYPE
  BRAZIL                       2                 21
  CANADA                       2                  3
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      2                  5
  UNITED STATES               23                155
  VIETNAM                      2                 12
[1] 7 2
[1] 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    2 14 15  0  2
  16P GAIN WILD-TYPE 15 92 82  1 12
D28V15, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  G1                2                 15
  G2               14                 92
  G3               15                 82
  G4                0                  1
  GX                2                 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"
D28V16, continuous
D28V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16P GAIN MUTATED                                             2
  16P GAIN WILD-TYPE                                          29
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16P GAIN MUTATED                8                  16
  16P GAIN WILD-TYPE             44                  96
D28V18, multiclass
                                                 clus
vv                                                16P 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                                                 8
  LIFELONG NON-SMOKER                                           16
                                                 clus
vv                                                16P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  44
  LIFELONG NON-SMOKER                                             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"
D28V19, continuous
D28V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  16P GAIN MUTATED             3       10             1        0
  16P GAIN WILD-TYPE          16       65            11       12
D28V21, multiclass
               clus
vv              16P GAIN MUTATED 16P GAIN WILD-TYPE
  COMBINATION                  3                 16
  EXTERNAL                    10                 65
  EXTERNAL BEAM                1                 11
  INTERNAL                     0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V22, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  0
  16P GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    0
  16P GAIN WILD-TYPE   21    3
                         clus
vv                        16P GAIN MUTATED 16P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  16P GAIN MUTATED                    0                0                   3
  16P GAIN WILD-TYPE                  2                2                  25
                    vv
clus                 REGIONAL SITE
  16P GAIN MUTATED               0
  16P GAIN WILD-TYPE            16
D28V23, multiclass
                     clus
vv                    16P GAIN MUTATED 16P GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                3                 25
  REGIONAL SITE                      0                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V24, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3  0
  16P GAIN WILD-TYPE 31  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    0
  16P GAIN WILD-TYPE   31    3
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  CGY                3                 31
  GY                 0                  3
[1] 2 2
[1] FALSE
D28V25, continuous
D28V26, continuous
D28V27, continuous
D28V28, continuous
D28V29, continuous
D28V30, 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                         4                       0
  16P GAIN WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16P GAIN MUTATED                         1
  16P GAIN WILD-TYPE                       6
D28V31, multiclass
                                     clus
vv                                    16P GAIN MUTATED 16P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            4                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  16P GAIN MUTATED                                               0
  16P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  16P GAIN MUTATED                                                4
  16P GAIN WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16P GAIN MUTATED                                                                                   8
  16P GAIN WILD-TYPE                                                                                60
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16P GAIN MUTATED                                                                                             15
  16P GAIN WILD-TYPE                                                                                           90
D28V32, multiclass
                                                                                              clus
vv                                                                                             16P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               15
                                                                                              clus
vv                                                                                             16P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V33, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   11 10
  16P GAIN WILD-TYPE 57 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     11   10
  16P GAIN WILD-TYPE   57   60
         clus
vv        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ABSENT                11                 57
  PRESENT               10                 60
[1] 2 2
[1] FALSE
D28V34, continuous
D28V35, continuous
D28V36, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4 18
  16P GAIN WILD-TYPE 39 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   18
  16P GAIN WILD-TYPE   39   76
                                          clus
vv                                         16P GAIN MUTATED 16P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               18                 76
[1] 2 2
[1] FALSE
D28V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16P GAIN MUTATED              0           5          9
  16P GAIN WILD-TYPE           10          44         48
D28V38, multiclass
              clus
vv             16P GAIN MUTATED 16P GAIN WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 5                 44
  NEVER USED                  9                 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"
D28V39, continuous
D28V40, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    9  4
  16P GAIN WILD-TYPE 80 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    4
  16P GAIN WILD-TYPE   80   12
         clus
vv        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ABSENT                 9                 80
  PRESENT                4                 12
[1] 2 2
[1] FALSE
D28V41, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1ML         TCGA-C5-A1MN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  16P GAIN MUTATED     0    0   3   11    3  0   2    3    1   3  1   2  0   0
  16P GAIN WILD-TYPE   1    1  27   54   21  4   6    4    8  19  0   6  2   1
                    vv
clus                 TX
  16P GAIN MUTATED    0
  16P GAIN WILD-TYPE 14
D28V42, multiclass
      clus
vv     16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 3                 27
  T1B1               11                 54
  T1B2                3                 21
  T2                  0                  4
  T2A                 2                  6
  T2A1                3                  4
  T2A2                1                  8
  T2B                 3                 19
  T3                  1                  0
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  16P GAIN MUTATED         0        0         0         0        4         9
  16P GAIN WILD-TYPE       4        2         1         1       27        60
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  16P GAIN MUTATED           4        1         0          2          1
  16P GAIN WILD-TYPE        28        2         6          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  16P GAIN MUTATED           5         1          6         0         0
  16P GAIN WILD-TYPE        22         0         28         3         7
D28V44, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 27
  STAGE IB1                 9                 60
  STAGE IB2                 4                 28
  STAGE II                  1                  2
  STAGE IIA                 0                  6
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                 5                 22
  STAGE III                 1                  0
  STAGE IIIB                6                 28
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    21   8
  16Q GAIN WILD-TYPE 162  42
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                29                204 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                 42 
$`16Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A7CH 
       57.04        31.40        46.32        38.99        35.61       154.32 
TCGA-C5-A7UC TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A3LQ 
       17.19         2.73        27.52         1.12        58.88        22.98 
TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H1 
        8.28        13.05        14.50        14.96         0.36        26.27 
TCGA-EK-A2RM TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A40J TCGA-JW-A5VJ 
        2.24         6.94        19.79        23.84         1.35        21.44 
TCGA-JX-A3Q0 TCGA-PN-A8MA TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8QA 
      195.85         2.96        11.67        12.16        23.28 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        2.43        20.91        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-A7UE TCGA-C5-A7UH 
      134.33        15.48        20.35       147.35        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       75.78        99.91        23.51         6.12        20.91         4.47 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        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        17.52 
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-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S 
        1.18        14.50         1.35         1.35         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        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.99        13.58        13.48        12.59        45.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         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-EX-A8YF TCGA-FU-A23K 
       20.35         7.92        14.70         6.12         4.73         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-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11        30.31         7.99        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         5.49        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        5.88         6.25        10.39        19.59         3.88        93.99 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       61.28        10.03        34.52        29.03        20.22        14.07 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        53.52        32.15        46.03        11.51        49.55 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        16.64         4.73        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.36               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            195.85             182.93 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             19.79              15.58 
[1] "0.4 - 195.8 (19.8)" "0.0 - 182.9 (15.6)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                  T1  T2 T3+T4
  16Q GAIN MUTATED    13   8     3
  16Q GAIN WILD-TYPE 108  42     8
D29V3, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                  13                108
  T2                   8                 42
  T3+T4                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   14  8
  16Q GAIN WILD-TYPE 97 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     14    8
  16Q GAIN WILD-TYPE   97   39
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               14                 97
  1                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED   17  0  7
  16Q GAIN WILD-TYPE 74  8 86
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               17                 74
  M1                0                  8
  MX                7                 86
[1] 3 2
[1] 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               1                               26
  16Q GAIN WILD-TYPE             4                              171
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16Q GAIN MUTATED                                               0
  16Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16Q GAIN MUTATED                                     1
  16Q GAIN WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16Q GAIN MUTATED                                           0
  16Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16Q GAIN MUTATED                                              1
  16Q GAIN WILD-TYPE                                            5
D29V6, multiclass
                                               clus
vv                                              16Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            26
  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                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             171
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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  25
  16Q GAIN WILD-TYPE  26 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   25
  16Q GAIN WILD-TYPE   26  183
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 4                 26
  YES               25                183
[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                                6    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED                           2
  16Q GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           0    18
  16Q GAIN WILD-TYPE                                         1   151
D29V10, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                2                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   18                151
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  18
  16Q GAIN WILD-TYPE  15 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   18
  16Q GAIN WILD-TYPE   15  131
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               18                131
[1] 2 2
[1] FALSE
D29V12, continuous
D29V13, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    8  6
  16Q GAIN WILD-TYPE 63 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      8    6
  16Q GAIN WILD-TYPE   63   19
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  TUMOR FREE                8                 63
  WITH TUMOR                6                 19
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  16Q GAIN MUTATED        1      2       1      0       1            22       2
  16Q GAIN WILD-TYPE     22      3       0     10       6           156      12
D29V14, multiclass
               clus
vv              16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  BRAZIL                       1                 22
  CANADA                       2                  3
  NIGERIA                      1                  0
  RUSSIA                       0                 10
  UKRAINE                      1                  6
  UNITED STATES               22                156
  VIETNAM                      2                 12
[1] 7 2
[1] 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    1  9 17  0  2
  16Q GAIN WILD-TYPE 16 97 80  1 12
D29V15, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  G1                1                 16
  G2                9                 97
  G3               17                 80
  G4                0                  1
  GX                2                 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"
D29V16, continuous
D29V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16Q GAIN MUTATED                                             2
  16Q GAIN WILD-TYPE                                          29
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16Q GAIN MUTATED                6                  14
  16Q GAIN WILD-TYPE             46                  98
D29V18, multiclass
                                                 clus
vv                                                16Q 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                                                 6
  LIFELONG NON-SMOKER                                           14
                                                 clus
vv                                                16Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  46
  LIFELONG NON-SMOKER                                             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"
D29V19, continuous
D29V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  16Q GAIN MUTATED             3        9             1        1
  16Q GAIN WILD-TYPE          16       66            11       11
D29V21, multiclass
               clus
vv              16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COMBINATION                  3                 16
  EXTERNAL                     9                 66
  EXTERNAL BEAM                1                 11
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V22, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  0
  16Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    0
  16Q GAIN WILD-TYPE   21    3
                         clus
vv                        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  16Q GAIN MUTATED                    0                0                   3
  16Q GAIN WILD-TYPE                  2                2                  25
                    vv
clus                 REGIONAL SITE
  16Q GAIN MUTATED               0
  16Q GAIN WILD-TYPE            16
D29V23, multiclass
                     clus
vv                    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                3                 25
  REGIONAL SITE                      0                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V24, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  0
  16Q GAIN WILD-TYPE 31  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    0
  16Q GAIN WILD-TYPE   31    3
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CGY                3                 31
  GY                 0                  3
[1] 2 2
[1] FALSE
D29V25, continuous
D29V26, continuous
D29V27, continuous
D29V28, continuous
D29V29, continuous
D29V30, 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                         5                       0
  16Q GAIN WILD-TYPE                      24                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16Q GAIN MUTATED                         1
  16Q GAIN WILD-TYPE                       6
D29V31, multiclass
                                     clus
vv                                    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            5                 24
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  16Q GAIN MUTATED                                               0
  16Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  16Q GAIN MUTATED                                                3
  16Q GAIN WILD-TYPE                                             13
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16Q GAIN MUTATED                                                                                   6
  16Q GAIN WILD-TYPE                                                                                62
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16Q GAIN MUTATED                                                                                             14
  16Q GAIN WILD-TYPE                                                                                           91
D29V32, multiclass
                                                                                              clus
vv                                                                                             16Q 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)                           6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               14
                                                                                              clus
vv                                                                                             16Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V33, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    8 10
  16Q GAIN WILD-TYPE 60 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      8   10
  16Q GAIN WILD-TYPE   60   60
         clus
vv        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ABSENT                 8                 60
  PRESENT               10                 60
[1] 2 2
[1] FALSE
D29V34, continuous
D29V35, continuous
D29V36, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4 17
  16Q GAIN WILD-TYPE 39 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   17
  16Q GAIN WILD-TYPE   39   77
                                          clus
vv                                         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               17                 77
[1] 2 2
[1] FALSE
D29V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16Q GAIN MUTATED              1           6          6
  16Q GAIN WILD-TYPE            9          43         51
D29V38, multiclass
              clus
vv             16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 6                 43
  NEVER USED                  6                 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"
D29V39, continuous
D29V40, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    8  2
  16Q GAIN WILD-TYPE 81 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      8    2
  16Q GAIN WILD-TYPE   81   14
         clus
vv        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ABSENT                 8                 81
  PRESENT                2                 14
[1] 2 2
[1] FALSE
D29V41, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1ML         TCGA-C5-A1MN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  16Q GAIN MUTATED     0    0   5    7    1  0   1    4    1   2  1   2  0   0
  16Q GAIN WILD-TYPE   1    1  25   58   23  4   7    3    8  20  0   6  2   1
                    vv
clus                 TX
  16Q GAIN MUTATED    0
  16Q GAIN WILD-TYPE 14
D29V42, multiclass
      clus
vv     16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 5                 25
  T1B1                7                 58
  T1B2                1                 23
  T2                  0                  4
  T2A                 1                  7
  T2A1                4                  3
  T2A2                1                  8
  T2B                 2                 20
  T3                  1                  0
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  16Q GAIN MUTATED         0        0         0         0        6         6
  16Q GAIN WILD-TYPE       4        2         1         1       25        63
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  16Q GAIN MUTATED           2        0         0          3          1
  16Q GAIN WILD-TYPE        30        3         6          2          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  16Q GAIN MUTATED           4         1          6         0         0
  16Q GAIN WILD-TYPE        23         0         28         3         7
D29V44, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 25
  STAGE IB1                 6                 63
  STAGE IB2                 2                 30
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                3                  2
  STAGE IIA2                1                  6
  STAGE IIB                 4                 23
  STAGE III                 1                  0
  STAGE IIIB                6                 28
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    14   4
  17P GAIN WILD-TYPE 169  46
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                215 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 46 
$`17P GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A7CH TCGA-C5-A7UE 
       23.67        31.40        35.01        35.61       154.32        85.55 
TCGA-DG-A2KH TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EK-A2PM TCGA-FU-A40J TCGA-JX-A5QV 
        1.12        22.98         1.32         0.59         1.35         7.99 
TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A9U5 
        5.49        15.95        93.99        34.52        19.96        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        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        20.35       147.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       60.69        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35        75.78        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
        6.12        20.91         4.47        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        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        17.52         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-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        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.99        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 
       45.96        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
        6.71        21.11       195.85        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        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        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       13.35         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       12.16        61.28        10.03        29.03        20.22        14.07 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       53.52        32.15        46.03        23.28        11.51        49.55 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        16.64         4.73        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        18.05 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.59               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            154.32             195.85 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            23.325             15.480 
[1] "0.6 - 154.3 (23.3)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                  T1  T2 T3+T4
  17P GAIN MUTATED     5   4     3
  17P GAIN WILD-TYPE 116  46     8
D30V3, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                   5                116
  T2                   4                 46
  T3+T4                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5   5
  17P GAIN WILD-TYPE 106  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    5
  17P GAIN WILD-TYPE  106   42
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                5                106
  1                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17P GAIN MUTATED    9  2  3
  17P GAIN WILD-TYPE 82  6 90
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                9                 82
  M1                2                  6
  MX                3                 90
[1] 3 2
[1] 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               1                               15
  17P GAIN WILD-TYPE             4                              182
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17P GAIN MUTATED                                               0
  17P GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17P GAIN MUTATED                                     2
  17P GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17P GAIN MUTATED                                           0
  17P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17P GAIN MUTATED                                              0
  17P GAIN WILD-TYPE                                            6
D30V6, multiclass
                                               clus
vv                                              17P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  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                                              17P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             182
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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  14
  17P GAIN WILD-TYPE  26 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   14
  17P GAIN WILD-TYPE   26  194
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 4                 26
  YES               14                194
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 71 
        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-A1ML 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LS         TCGA-C5-A2LT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UI         TCGA-C5-A7X8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7XC         TCGA-C5-A8XH         TCGA-C5-A8XI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A8YQ         TCGA-C5-A8YT         TCGA-C5-A8ZZ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DG-A2KL         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-GH-A9DA         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-JW-AAVH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-MU-A5YI         TCGA-MU-A8JM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73Q         TCGA-Q1-A73S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-VS-A8EH         TCGA-VS-A8QM         TCGA-VS-A94Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-WL-A834 
"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                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED                           1
  17P GAIN WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    14
  17P GAIN WILD-TYPE                                         1   155
D30V10, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 18
  BLACK OR AFRICAN AMERICAN                                1                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                155
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1   8
  17P GAIN WILD-TYPE  15 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    8
  17P GAIN WILD-TYPE   15  141
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO                8                141
[1] 2 2
[1] FALSE
D30V12, continuous
D30V13, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  3
  17P GAIN WILD-TYPE 67 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    3
  17P GAIN WILD-TYPE   67   22
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  TUMOR FREE                4                 67
  WITH TUMOR                3                 22
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  17P GAIN MUTATED        3      1       0      1       0            13       0
  17P GAIN WILD-TYPE     20      4       1      9       7           165      14
D30V14, multiclass
               clus
vv              17P GAIN MUTATED 17P GAIN WILD-TYPE
  BRAZIL                       3                 20
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  7
  UNITED STATES               13                165
  VIETNAM                      0                 14
[1] 7 2
[1] 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  7 10  0  1
  17P GAIN WILD-TYPE 17 99 87  1 13
D30V15, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  G1                0                 17
  G2                7                 99
  G3               10                 87
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V16, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 33 
        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-C5-A8XH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A907         TCGA-DG-A2KK         TCGA-EK-A2RA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EX-A69M         TCGA-FU-A2QG         TCGA-FU-A3TX 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-HM-A3JK         TCGA-HM-A4S6 
"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-JX-A3Q0         TCGA-MU-A5YI         TCGA-MU-A8JM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73S         TCGA-RA-A741 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-VS-A8QF         TCGA-VS-A94Z         TCGA-WL-A834 
"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                 71 
        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-A1ML 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LS         TCGA-C5-A2LT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UI         TCGA-C5-A7X8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7XC         TCGA-C5-A8XH         TCGA-C5-A8XI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A8YQ         TCGA-C5-A8YT         TCGA-C5-A8ZZ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DG-A2KL         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-GH-A9DA         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-JW-AAVH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-MU-A5YI         TCGA-MU-A8JM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73Q         TCGA-Q1-A73S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD         TCGA-UC-A7PG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-VS-A8EH         TCGA-VS-A8QM         TCGA-VS-A94Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-WL-A834 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17P GAIN MUTATED                                             1
  17P GAIN WILD-TYPE                                          30
                    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                                                 1
  17P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17P GAIN MUTATED                3                   9
  17P GAIN WILD-TYPE             49                 103
D30V18, multiclass
                                                 clus
vv                                                17P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                            9
                                                 clus
vv                                                17P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  49
  LIFELONG NON-SMOKER                                            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"
D30V19, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 65 
        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-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-C5-A907         TCGA-DG-A2KK 
"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-EK-A2RA         TCGA-EX-A1H5         TCGA-FU-A2QG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         TCGA-GH-A9DA 
"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-JW-AAVH         TCGA-JX-A3Q0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-RA-A741 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PG         TCGA-VS-A8EH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-VS-A8QF         TCGA-VS-A8QM         TCGA-VS-A94Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-WL-A834 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  17P GAIN MUTATED             2        5             2        2
  17P GAIN WILD-TYPE          17       70            10       10
D30V21, multiclass
               clus
vv              17P GAIN MUTATED 17P GAIN WILD-TYPE
  COMBINATION                  2                 17
  EXTERNAL                     5                 70
  EXTERNAL BEAM                2                 10
  INTERNAL                     2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V22, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  0
  17P GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    0
  17P GAIN WILD-TYPE   21    3
                         clus
vv                        17P GAIN MUTATED 17P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  17P GAIN MUTATED                    0                0                   4
  17P GAIN WILD-TYPE                  2                2                  24
                    vv
clus                 REGIONAL SITE
  17P GAIN MUTATED               1
  17P GAIN WILD-TYPE            15
D30V23, multiclass
                     clus
vv                    17P GAIN MUTATED 17P GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                4                 24
  REGIONAL SITE                      1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V24, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  1
  17P GAIN WILD-TYPE 31  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    1
  17P GAIN WILD-TYPE   31    2
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  CGY                3                 31
  GY                 1                  2
[1] 2 2
[1] FALSE
D30V25, continuous
D30V26, continuous
D30V27, continuous
D30V28, continuous
D30V29, continuous
D30V30, 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                         2                       0
  17P GAIN WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17P GAIN MUTATED                         0
  17P GAIN WILD-TYPE                       7
D30V31, multiclass
                                     clus
vv                                    17P GAIN MUTATED 17P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            2                 27
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  17P GAIN MUTATED                                               0
  17P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17P GAIN MUTATED                                                3
  17P GAIN WILD-TYPE                                             13
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17P GAIN MUTATED                                                                                   5
  17P GAIN WILD-TYPE                                                                                63
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17P GAIN MUTATED                                                                                              7
  17P GAIN WILD-TYPE                                                                                           98
D30V32, multiclass
                                                                                              clus
vv                                                                                             17P 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)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                7
                                                                                              clus
vv                                                                                             17P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            63
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V33, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  6
  17P GAIN WILD-TYPE 65 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    6
  17P GAIN WILD-TYPE   65   64
         clus
vv        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ABSENT                 3                 65
  PRESENT                6                 64
[1] 2 2
[1] FALSE
D30V34, continuous
D30V35, continuous
D30V36, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  4
  17P GAIN WILD-TYPE 40 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    4
  17P GAIN WILD-TYPE   40   90
                                          clus
vv                                         17P GAIN MUTATED 17P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                4                 90
[1] 2 2
[1] FALSE
D30V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17P GAIN MUTATED              0           5          3
  17P GAIN WILD-TYPE           10          44         54
D30V38, multiclass
              clus
vv             17P GAIN MUTATED 17P GAIN WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 5                 44
  NEVER USED                  3                 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"
D30V39, continuous
D30V40, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    6  2
  17P GAIN WILD-TYPE 83 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6    2
  17P GAIN WILD-TYPE   83   14
         clus
vv        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ABSENT                 6                 83
  PRESENT                2                 14
[1] 2 2
[1] FALSE
D30V41, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A3JK         TCGA-JW-A852 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-MU-A51Y         TCGA-MU-A8JM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  17P GAIN MUTATED     0    0   0    5    0  0   1    1    0   2  0   3  0   1
  17P GAIN WILD-TYPE   1    1  30   60   24  4   7    6    9  20  1   5  2   0
                    vv
clus                 TX
  17P GAIN MUTATED    1
  17P GAIN WILD-TYPE 13
D30V42, multiclass
      clus
vv     17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 0                 30
  T1B1                5                 60
  T1B2                0                 24
  T2                  0                  4
  T2A                 1                  7
  T2A1                1                  6
  T2A2                0                  9
  T2B                 2                 20
  T3                  0                  1
  T3B                 3                  5
  T4                  0                  2
  TIS                 1                  0
  TX                  1                 13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  17P GAIN MUTATED         0        0         0         0        0         7
  17P GAIN WILD-TYPE       4        2         1         1       31        62
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  17P GAIN MUTATED           0        1         1          0          0
  17P GAIN WILD-TYPE        32        2         5          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  17P GAIN MUTATED           5         0          3         0         0
  17P GAIN WILD-TYPE        22         1         31         3         7
D30V44, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  0                 31
  STAGE IB1                 7                 62
  STAGE IB2                 0                 32
  STAGE II                  1                  2
  STAGE IIA                 1                  5
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 5                 22
  STAGE III                 0                  1
  STAGE IIIB                3                 31
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    30   5
  17Q GAIN WILD-TYPE 153  45
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                35                198 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 45 
$`17Q GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MP TCGA-C5-A2LZ 
       23.67        31.40        35.01        35.61         3.58       100.14 
TCGA-C5-A7CH TCGA-C5-A7UE TCGA-DG-A2KH TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EA-A3QD 
      154.32        85.55         1.12        22.98         1.32        13.05 
TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RM 
       14.50        14.96         0.59         0.13        16.08         2.24 
TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-FU-A40J TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV 
        0.10         6.94         1.35        10.06        30.31         7.99 
TCGA-LP-A4AU TCGA-MU-A51Y TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-UC-A7PF 
       11.28        13.87         5.49        13.35        15.95        93.99 
TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A94X TCGA-VS-A959 TCGA-VS-A9U5 
       34.52        14.07        16.64        39.35        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91        40.93        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-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-A7UH TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        4.47        58.88        50.76        44.94        40.04        87.75 
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        17.52         8.28         0.76        12.36         1.74 
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-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-EA-A97N 
       13.91        15.02        14.99        13.58        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       12.59        45.96        26.27         6.64         1.51         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.59         1.45         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-A3GN 
        1.18        23.70         0.10         0.07         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
       20.35         7.92        14.70        19.79         6.12         4.73 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AW TCGA-LP-A4AX 
        5.13         6.71        21.11       195.85         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.30         0.82         0.20         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        0.07         4.34         2.96        15.58         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
       19.59         3.88        11.67        12.16        61.28        10.03 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       29.03        20.22        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y 
       23.28        11.51        49.55        39.78        31.27         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-WL-A834 
       23.24        44.88        42.58        42.08        43.82        18.05 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.10               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            154.32             195.85 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.50              16.16 
[1] "0.1 - 154.3 (14.5)" "0.0 - 195.8 (16.2)"
[1] "hr=" "1.4"
D31V2, continuous
                    vv
clus                  T1  T2 T3+T4
  17Q GAIN MUTATED    12  10     4
  17Q GAIN WILD-TYPE 109  40     7
D31V3, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                  12                109
  T2                  10                 40
  T3+T4                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   12  8
  17Q GAIN WILD-TYPE 99 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12    8
  17Q GAIN WILD-TYPE   99   39
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               12                 99
  1                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   15  1 12
  17Q GAIN WILD-TYPE 76  7 81
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               15                 76
  M1                1                  7
  MX               12                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED               1                               29
  17Q GAIN WILD-TYPE             4                              168
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17Q GAIN MUTATED                                               0
  17Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17Q GAIN MUTATED                                     6
  17Q GAIN WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17Q GAIN MUTATED                                           0
  17Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17Q GAIN MUTATED                                              0
  17Q GAIN WILD-TYPE                                            6
D31V6, multiclass
                                               clus
vv                                              17Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            29
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              17Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             168
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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  32
  17Q GAIN WILD-TYPE  26 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   32
  17Q GAIN WILD-TYPE   26  176
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 4                 26
  YES               32                176
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     4
  17Q GAIN WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED                           3
  17Q GAIN WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    24
  17Q GAIN WILD-TYPE                                         1   145
D31V10, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                3                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   24                145
[1] 5 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     4  20
  17Q GAIN WILD-TYPE  12 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   20
  17Q GAIN WILD-TYPE   12  129
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               20                129
[1] 2 2
[1] FALSE
D31V12, continuous
D31V13, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   10  6
  17Q GAIN WILD-TYPE 61 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     10    6
  17Q GAIN WILD-TYPE   61   19
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  TUMOR FREE               10                 61
  WITH TUMOR                6                 19
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  17Q GAIN MUTATED        5      1       0      1       0            26       3
  17Q GAIN WILD-TYPE     18      4       1      9       7           152      11
D31V14, multiclass
               clus
vv              17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  BRAZIL                       5                 18
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  7
  UNITED STATES               26                152
  VIETNAM                      3                 11
[1] 7 2
[1] 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 12 21  0  3
  17Q GAIN WILD-TYPE 17 94 76  1 11
D31V15, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  G1                0                 17
  G2               12                 94
  G3               21                 76
  G4                0                  1
  GX                3                 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"
D31V16, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 32 
        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-C5-A8XH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-C5-A907         TCGA-DG-A2KK         TCGA-EX-A69M 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3TX         TCGA-FU-A3WB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-IR-A3L7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JX-A3Q0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-VS-A8QF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-WL-A834 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
D31V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17Q GAIN MUTATED                                             2
  17Q GAIN WILD-TYPE                                          29
                    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                                                 1
  17Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17Q GAIN MUTATED                4                  22
  17Q GAIN WILD-TYPE             48                  90
D31V18, multiclass
                                                 clus
vv                                                17Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                           22
                                                 clus
vv                                                17Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  48
  LIFELONG NON-SMOKER                                             90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V19, continuous
D31V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  17Q GAIN MUTATED             2       11             2        3
  17Q GAIN WILD-TYPE          17       64            10        9
D31V21, multiclass
               clus
vv              17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COMBINATION                  2                 17
  EXTERNAL                    11                 64
  EXTERNAL BEAM                2                 10
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V22, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    4  0
  17Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4    0
  17Q GAIN WILD-TYPE   21    3
                         clus
vv                        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  17Q GAIN MUTATED                    0                0                   7
  17Q GAIN WILD-TYPE                  2                2                  21
                    vv
clus                 REGIONAL SITE
  17Q GAIN MUTATED               3
  17Q GAIN WILD-TYPE            13
D31V23, multiclass
                     clus
vv                    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                7                 21
  REGIONAL SITE                      3                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V24, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    7  1
  17Q GAIN WILD-TYPE 27  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7    1
  17Q GAIN WILD-TYPE   27    2
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CGY                7                 27
  GY                 1                  2
[1] 2 2
[1] FALSE
D31V25, continuous
D31V26, continuous
D31V27, continuous
D31V28, continuous
D31V29, continuous
D31V30, 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                         3                       0
  17Q GAIN WILD-TYPE                      26                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17Q GAIN MUTATED                         0
  17Q GAIN WILD-TYPE                       7
D31V31, multiclass
                                     clus
vv                                    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            3                 26
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  17Q GAIN MUTATED                                               0
  17Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17Q GAIN MUTATED                                                4
  17Q GAIN WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17Q GAIN MUTATED                                                                                   9
  17Q GAIN WILD-TYPE                                                                                59
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17Q GAIN MUTATED                                                                                             15
  17Q GAIN WILD-TYPE                                                                                           90
D31V32, multiclass
                                                                                              clus
vv                                                                                             17Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               15
                                                                                              clus
vv                                                                                             17Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            59
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V33, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    8 12
  17Q GAIN WILD-TYPE 60 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      8   12
  17Q GAIN WILD-TYPE   60   58
         clus
vv        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ABSENT                 8                 60
  PRESENT               12                 58
[1] 2 2
[1] FALSE
D31V34, continuous
D31V35, continuous
D31V36, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    4 11
  17Q GAIN WILD-TYPE 39 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   11
  17Q GAIN WILD-TYPE   39   83
                                          clus
vv                                         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               11                 83
[1] 2 2
[1] FALSE
D31V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17Q GAIN MUTATED              2           9          6
  17Q GAIN WILD-TYPE            8          40         51
D31V38, multiclass
              clus
vv             17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                 9                 40
  NEVER USED                  6                 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"
D31V39, continuous
D31V40, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   12  4
  17Q GAIN WILD-TYPE 77 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12    4
  17Q GAIN WILD-TYPE   77   12
         clus
vv        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ABSENT                12                 77
  PRESENT                4                 12
[1] 2 2
[1] FALSE
D31V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  17Q GAIN MUTATED     0    0   0   10    2  1   1    4    1   3  0   4  0   1
  17Q GAIN WILD-TYPE   1    1  30   55   22  3   7    3    8  19  1   4  2   0
                    vv
clus                 TX
  17Q GAIN MUTATED    2
  17Q GAIN WILD-TYPE 12
D31V42, multiclass
      clus
vv     17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 0                 30
  T1B1               10                 55
  T1B2                2                 22
  T2                  1                  3
  T2A                 1                  7
  T2A1                4                  3
  T2A2                1                  8
  T2B                 3                 19
  T3                  0                  1
  T3B                 4                  4
  T4                  0                  2
  TIS                 1                  0
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  17Q GAIN MUTATED         0        0         0         0        1        11
  17Q GAIN WILD-TYPE       4        2         1         1       30        58
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  17Q GAIN MUTATED           2        1         2          3          1
  17Q GAIN WILD-TYPE        30        2         4          2          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  17Q GAIN MUTATED           7         0          6         0         0
  17Q GAIN WILD-TYPE        20         1         28         3         7
D31V44, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  1                 30
  STAGE IB1                11                 58
  STAGE IB2                 2                 30
  STAGE II                  1                  2
  STAGE IIA                 2                  4
  STAGE IIA1                3                  2
  STAGE IIA2                1                  6
  STAGE IIB                 7                 20
  STAGE III                 0                  1
  STAGE IIIB                6                 28
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    29   5
  18P GAIN WILD-TYPE 154  45
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                34                199 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 45 
$`18P GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A7CG 
       23.67       173.29        46.32        38.99        73.18       182.93 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A8XI TCGA-DR-A0ZL TCGA-DS-A3LQ 
       20.35        17.19        60.69         8.35        87.75        22.98 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2PM 
        1.35        14.50        13.91        14.96         0.36         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RO TCGA-EX-A8YF TCGA-FU-A3TX TCGA-HM-A3JK TCGA-JW-A5VK 
        0.13         0.07         4.73         1.48        20.78        20.48 
TCGA-JX-A5QV TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-UC-A7PG TCGA-VS-A8EH 
        7.99         4.34         5.49        15.95        12.16        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A9U5 
       14.07        19.96        11.51        38.96 

$`18P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       31.40        30.21        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
      134.33        15.48       147.35        85.55        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61         2.73        50.99        45.83        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK 
       58.88        50.76        44.94        40.04        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        17.52 
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-A43B 
        0.62        13.05         1.18        14.50         1.35         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        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.99        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA 
        6.64         1.51         0.43         0.59         1.45        16.08 
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        19.79         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 
        1.12         9.01        25.41         7.13        21.67        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85        30.31        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       29.72         0.07         2.96        15.58        13.35         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         5.88         6.25 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       10.39        19.59         3.88        11.67        93.99        61.28 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       10.03        34.52        29.03        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-WL-A834 
       18.05 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.07               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            182.93             195.85 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            15.455             15.880 
[1] "0.1 - 182.9 (15.5)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                  T1  T2 T3+T4
  18P GAIN MUTATED    16   6     4
  18P GAIN WILD-TYPE 105  44     7
D32V3, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                  16                105
  T2                   6                 44
  T3+T4                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   17  4
  18P GAIN WILD-TYPE 94 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     17    4
  18P GAIN WILD-TYPE   94   43
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               17                 94
  1                4                 43
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18P GAIN MUTATED   16  2 10
  18P GAIN WILD-TYPE 75  6 83
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               16                 75
  M1                2                  6
  MX               10                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED               0                               33
  18P GAIN WILD-TYPE             5                              164
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18P GAIN MUTATED                                               1
  18P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18P GAIN MUTATED                                     0
  18P GAIN WILD-TYPE                                  22
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18P GAIN MUTATED                                           0
  18P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18P GAIN MUTATED                                              0
  18P GAIN WILD-TYPE                                            6
D32V6, multiclass
                                               clus
vv                                              18P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            33
  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                                              18P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             164
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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     5  29
  18P GAIN WILD-TYPE  25 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   29
  18P GAIN WILD-TYPE   25  179
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 5                 25
  YES               29                179
[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                                7    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED                           3
  18P GAIN WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0    24
  18P GAIN WILD-TYPE                                         1   145
D32V10, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                3                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   24                145
[1] 5 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     3  19
  18P GAIN WILD-TYPE  13 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   19
  18P GAIN WILD-TYPE   13  130
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               19                130
[1] 2 2
[1] FALSE
D32V12, continuous
D32V13, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   11  2
  18P GAIN WILD-TYPE 60 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     11    2
  18P GAIN WILD-TYPE   60   23
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  TUMOR FREE               11                 60
  WITH TUMOR                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  18P GAIN MUTATED        5      0       0      1       2            24       2
  18P GAIN WILD-TYPE     18      5       1      9       5           154      12
D32V14, multiclass
               clus
vv              18P GAIN MUTATED 18P GAIN WILD-TYPE
  BRAZIL                       5                 18
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      2                  5
  UNITED STATES               24                154
  VIETNAM                      2                 12
[1] 7 2
[1] 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    3 11 19  0  1
  18P GAIN WILD-TYPE 14 95 78  1 13
D32V15, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  G1                3                 14
  G2               11                 95
  G3               19                 78
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V16, continuous
D32V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18P GAIN MUTATED                                             4
  18P GAIN WILD-TYPE                                          27
                    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                                                 1
  18P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18P GAIN MUTATED                6                  15
  18P GAIN WILD-TYPE             46                  97
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                1
  CURRENT SMOKER                                                 6
  LIFELONG NON-SMOKER                                           15
                                                 clus
vv                                                18P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  46
  LIFELONG NON-SMOKER                                             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"
D32V19, continuous
D32V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  18P GAIN MUTATED             2       11             3        3
  18P GAIN WILD-TYPE          17       64             9        9
D32V21, multiclass
               clus
vv              18P GAIN MUTATED 18P GAIN WILD-TYPE
  COMBINATION                  2                 17
  EXTERNAL                    11                 64
  EXTERNAL BEAM                3                  9
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V22, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  0
  18P GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    0
  18P GAIN WILD-TYPE   21    3
                         clus
vv                        18P GAIN MUTATED 18P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  18P GAIN MUTATED                    0                0                   6
  18P GAIN WILD-TYPE                  2                2                  22
                    vv
clus                 REGIONAL SITE
  18P GAIN MUTATED               3
  18P GAIN WILD-TYPE            13
D32V23, multiclass
                     clus
vv                    18P GAIN MUTATED 18P GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                6                 22
  REGIONAL SITE                      3                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V24, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    7  1
  18P GAIN WILD-TYPE 27  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    1
  18P GAIN WILD-TYPE   27    2
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  CGY                7                 27
  GY                 1                  2
[1] 2 2
[1] FALSE
D32V25, continuous
D32V26, continuous
D32V27, continuous
D32V28, continuous
D32V29, continuous
D32V30, 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                         5                       0
  18P GAIN WILD-TYPE                      24                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18P GAIN MUTATED                         0
  18P GAIN WILD-TYPE                       7
D32V31, multiclass
                                     clus
vv                                    18P GAIN MUTATED 18P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                1                  1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            5                 24
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  18P GAIN MUTATED                                               0
  18P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18P GAIN MUTATED                                                4
  18P GAIN WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18P GAIN MUTATED                                                                                  11
  18P GAIN WILD-TYPE                                                                                57
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18P GAIN MUTATED                                                                                             13
  18P GAIN WILD-TYPE                                                                                           92
D32V32, multiclass
                                                                                              clus
vv                                                                                             18P 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)                          11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               13
                                                                                              clus
vv                                                                                             18P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V33, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   10  8
  18P GAIN WILD-TYPE 58 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     10    8
  18P GAIN WILD-TYPE   58   62
         clus
vv        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ABSENT                10                 58
  PRESENT                8                 62
[1] 2 2
[1] FALSE
D32V34, continuous
D32V35, continuous
D32V36, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    7 16
  18P GAIN WILD-TYPE 36 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7   16
  18P GAIN WILD-TYPE   36   78
                                          clus
vv                                         18P GAIN MUTATED 18P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    7                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               16                 78
[1] 2 2
[1] FALSE
D32V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18P GAIN MUTATED              1           5         12
  18P GAIN WILD-TYPE            9          44         45
D32V38, multiclass
              clus
vv             18P GAIN MUTATED 18P GAIN WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 5                 44
  NEVER USED                 12                 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"
D32V39, continuous
D32V40, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   10  2
  18P GAIN WILD-TYPE 79 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     10    2
  18P GAIN WILD-TYPE   79   14
         clus
vv        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ABSENT                10                 79
  PRESENT                2                 14
[1] 2 2
[1] FALSE
D32V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  18P GAIN MUTATED     0    0   5    6    5  0   0    2    1   3  0   4  0   1
  18P GAIN WILD-TYPE   1    1  25   59   19  4   8    5    8  19  1   4  2   0
                    vv
clus                 TX
  18P GAIN MUTATED    2
  18P GAIN WILD-TYPE 12
D32V42, multiclass
      clus
vv     18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 5                 25
  T1B1                6                 59
  T1B2                5                 19
  T2                  0                  4
  T2A                 0                  8
  T2A1                2                  5
  T2A2                1                  8
  T2B                 3                 19
  T3                  0                  1
  T3B                 4                  4
  T4                  0                  2
  TIS                 1                  0
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  18P GAIN MUTATED         0        0         0         0        6         6
  18P GAIN WILD-TYPE       4        2         1         1       25        63
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  18P GAIN MUTATED           6        0         1          1          2
  18P GAIN WILD-TYPE        26        3         5          4          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  18P GAIN MUTATED           5         0          5         1         0
  18P GAIN WILD-TYPE        22         1         29         2         7
D32V44, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 25
  STAGE IB1                 6                 63
  STAGE IB2                 6                 26
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                1                  4
  STAGE IIA2                2                  5
  STAGE IIB                 5                 22
  STAGE III                 0                  1
  STAGE IIIB                5                 29
  STAGE IVA                 1                  2
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    18   3
  18Q GAIN WILD-TYPE 165  47
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                212 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 47 
$`18Q GAIN MUTATED`
TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7UH TCGA-C5-A8XI TCGA-DS-A3LQ 
       38.99        73.18       182.93        60.69         8.35        22.98 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2R9 TCGA-EK-A2RO 
        1.35        14.50        14.96         0.36         0.13         0.07 
TCGA-FU-A3TX TCGA-HM-A3JK TCGA-JW-A5VK TCGA-JX-A5QV TCGA-MY-A913 TCGA-UC-A7PG 
        1.48        20.78        20.48         7.99         5.49        12.16 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QC 
       20.22        14.07        11.51 

$`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-A1ML 
       57.73        53.16        35.61         0.46         2.43        20.91 
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-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-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19        85.55        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99        45.83        75.78        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52         6.12        20.91         4.47         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        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        17.52 
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-A43B 
        0.62        13.05         1.18        14.50         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 
       15.02        14.99        13.58        13.48        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.18        23.70         2.24         0.10         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        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        6.12         4.73         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-A3YQ 
        0.66         1.02         1.45         1.58         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
        1.35         1.32         1.97         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
        7.13        21.67        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89         0.07         0.30         0.82         0.20 
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        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB 
       19.59         3.88        11.67        93.99        61.28        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       34.52        29.03        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.07               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            182.93             195.85 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             14.07              16.11 
[1] "0.1 - 182.9 (14.1)" "0.0 - 195.8 (16.1)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                  T1  T2 T3+T4
  18Q GAIN MUTATED    10   2     4
  18Q GAIN WILD-TYPE 111  48     7
D33V3, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                  10                111
  T2                   2                 48
  T3+T4                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    10   3
  18Q GAIN WILD-TYPE 101  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     10    3
  18Q GAIN WILD-TYPE  101   44
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               10                101
  1                3                 44
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED   10  1  6
  18Q GAIN WILD-TYPE 81  7 87
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0               10                 81
  M1                1                  7
  MX                6                 87
[1] 3 2
[1] 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                               21
  18Q GAIN WILD-TYPE             5                              176
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18Q GAIN MUTATED                                               0
  18Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18Q GAIN MUTATED                                     0
  18Q GAIN WILD-TYPE                                  22
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18Q GAIN MUTATED                                           0
  18Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18Q GAIN MUTATED                                              0
  18Q GAIN WILD-TYPE                                            6
D33V6, multiclass
                                               clus
vv                                              18Q 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                 0
                                               clus
vv                                              18Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             176
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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  17
  18Q GAIN WILD-TYPE  26 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4   17
  18Q GAIN WILD-TYPE   26  191
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 4                 26
  YES               17                191
[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                                7    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED                           3
  18Q GAIN WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    12
  18Q GAIN WILD-TYPE                                         1   157
D33V10, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                3                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   12                157
[1] 5 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     2  12
  18Q GAIN WILD-TYPE  14 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   12
  18Q GAIN WILD-TYPE   14  137
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               12                137
[1] 2 2
[1] FALSE
D33V12, continuous
D33V13, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  2
  18Q GAIN WILD-TYPE 67 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    2
  18Q GAIN WILD-TYPE   67   23
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  TUMOR FREE                4                 67
  WITH TUMOR                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  18Q GAIN MUTATED        3      0       0      1       1            14       2
  18Q GAIN WILD-TYPE     20      5       1      9       6           164      12
D33V14, multiclass
               clus
vv              18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  BRAZIL                       3                 20
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      1                  6
  UNITED STATES               14                164
  VIETNAM                      2                 12
[1] 7 2
[1] 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     2   6  12   0   1
  18Q GAIN WILD-TYPE  15 100  85   1  13
D33V15, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  G1                2                 15
  G2                6                100
  G3               12                 85
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V16, continuous
D33V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18Q GAIN MUTATED                                             2
  18Q GAIN WILD-TYPE                                          29
                    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                                                 1
  18Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18Q GAIN MUTATED                5                   8
  18Q GAIN WILD-TYPE             47                 104
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                1
  CURRENT SMOKER                                                 5
  LIFELONG NON-SMOKER                                            8
                                                 clus
vv                                                18Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  47
  LIFELONG NON-SMOKER                                            104
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V19, continuous
D33V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  18Q GAIN MUTATED             1        5             3        3
  18Q GAIN WILD-TYPE          18       70             9        9
D33V21, multiclass
               clus
vv              18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COMBINATION                  1                 18
  EXTERNAL                     5                 70
  EXTERNAL BEAM                3                  9
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V22, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  0
  18Q GAIN WILD-TYPE 22  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    0
  18Q GAIN WILD-TYPE   22    3
                         clus
vv                        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   3                 22
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  18Q GAIN MUTATED                    0                0                   4
  18Q GAIN WILD-TYPE                  2                2                  24
                    vv
clus                 REGIONAL SITE
  18Q GAIN MUTATED               3
  18Q GAIN WILD-TYPE            13
D33V23, multiclass
                     clus
vv                    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                4                 24
  REGIONAL SITE                      3                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V24, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  1
  18Q GAIN WILD-TYPE 29  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    1
  18Q GAIN WILD-TYPE   29    2
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CGY                5                 29
  GY                 1                  2
[1] 2 2
[1] FALSE
D33V25, continuous
D33V26, continuous
D33V27, continuous
D33V28, continuous
D33V29, continuous
D33V30, 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                         3                       0
  18Q GAIN WILD-TYPE                      26                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18Q GAIN MUTATED                         0
  18Q GAIN WILD-TYPE                       7
D33V31, multiclass
                                     clus
vv                                    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                1                  1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            3                 26
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  18Q GAIN MUTATED                                               0
  18Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18Q GAIN MUTATED                                                3
  18Q GAIN WILD-TYPE                                             13
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18Q GAIN MUTATED                                                                                   6
  18Q GAIN WILD-TYPE                                                                                62
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18Q GAIN MUTATED                                                                                              9
  18Q GAIN WILD-TYPE                                                                                           96
D33V32, multiclass
                                                                                              clus
vv                                                                                             18Q 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)                           6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                9
                                                                                              clus
vv                                                                                             18Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V33, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  4
  18Q GAIN WILD-TYPE 61 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    4
  18Q GAIN WILD-TYPE   61   66
         clus
vv        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ABSENT                 7                 61
  PRESENT                4                 66
[1] 2 2
[1] FALSE
D33V34, continuous
D33V35, continuous
D33V36, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    6  8
  18Q GAIN WILD-TYPE 37 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    8
  18Q GAIN WILD-TYPE   37   86
                                          clus
vv                                         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                8                 86
[1] 2 2
[1] FALSE
D33V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18Q GAIN MUTATED              1           4          7
  18Q GAIN WILD-TYPE            9          45         50
D33V38, multiclass
              clus
vv             18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 4                 45
  NEVER USED                  7                 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"
D33V39, continuous
D33V40, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    6  1
  18Q GAIN WILD-TYPE 83 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    1
  18Q GAIN WILD-TYPE   83   15
         clus
vv        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ABSENT                 6                 83
  PRESENT                1                 15
[1] 2 2
[1] FALSE
D33V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  18Q GAIN MUTATED     0    0   2    4    4  0   0    1    0   1  0   4  0   1
  18Q GAIN WILD-TYPE   1    1  28   61   20  4   8    6    9  21  1   4  2   0
                    vv
clus                 TX
  18Q GAIN MUTATED    1
  18Q GAIN WILD-TYPE 13
D33V42, multiclass
      clus
vv     18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 2                 28
  T1B1                4                 61
  T1B2                4                 20
  T2                  0                  4
  T2A                 0                  8
  T2A1                1                  6
  T2A2                0                  9
  T2B                 1                 21
  T3                  0                  1
  T3B                 4                  4
  T4                  0                  2
  TIS                 1                  0
  TX                  1                 13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  18Q GAIN MUTATED         0        0         0         0        2         4
  18Q GAIN WILD-TYPE       4        2         1         1       29        65
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  18Q GAIN MUTATED           4        0         1          1          1
  18Q GAIN WILD-TYPE        28        3         5          4          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  18Q GAIN MUTATED           2         0          5         1         0
  18Q GAIN WILD-TYPE        25         1         29         2         7
D33V44, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  2                 29
  STAGE IB1                 4                 65
  STAGE IB2                 4                 28
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                1                  4
  STAGE IIA2                1                  6
  STAGE IIB                 2                 25
  STAGE III                 0                  1
  STAGE IIIB                5                 29
  STAGE IVA                 1                  2
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    33   6
  19P GAIN WILD-TYPE 150  44
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                39                194 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 44 
$`19P GAIN MUTATED`
TCGA-C5-A0TN TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A7CG 
       11.44        53.16        38.99        78.35        52.01       182.93 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7X5 TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KL 
      154.32       134.33        13.61         4.47        58.88        44.94 
TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
        2.66        22.98         8.28        13.91        14.96         0.36 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RM TCGA-EK-A2RN TCGA-FU-A40J TCGA-HG-A9SC 
        0.59         0.59         2.24         0.10         1.35         7.13 
TCGA-HM-A3JK TCGA-IR-A3LL TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A7HU 
       20.78        36.36       195.85        11.28         0.30         0.20 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8QF 
        0.07         5.49        15.95        12.16        14.07        49.55 
TCGA-VS-A954 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        38.96        18.05 

$`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-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        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-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL 
        0.82        18.02        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 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34         2.73        50.99        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH 
       99.91        23.51        27.52         6.12        20.91         1.12 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       50.76        40.04        87.75        58.88        36.76       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT 
      118.65        16.83        16.18        17.52         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-A5ZD TCGA-EA-A5ZE 
       12.82         0.26        14.89         1.48        15.02        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        1.51         0.43         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO 
        4.04         0.03         0.36         1.18        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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        9.01        25.41        21.67        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 
       15.58        10.06         5.13         6.71        21.11        30.31 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        7.99         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        15.58        13.35 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        3.39        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        10.39        19.59         3.88        11.67        93.99 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ 
       61.28        10.03        34.52        29.03        20.22        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH 
       53.52        32.15        46.03        23.28        11.51        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 
       31.27        16.64         4.73        23.24        44.88        42.08 
TCGA-VS-A958 TCGA-VS-A959 
       43.82        39.35 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            195.85             177.04 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             14.07              16.11 
[1] "0.1 - 195.8 (14.1)" "0.0 - 177.0 (16.1)"
[1] "hr=" "1.6"
D34V2, continuous
                    vv
clus                  T1  T2 T3+T4
  19P GAIN MUTATED    13  10     5
  19P GAIN WILD-TYPE 108  40     6
D34V3, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                  13                108
  T2                  10                 40
  T3+T4                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   13 12
  19P GAIN WILD-TYPE 98 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13   12
  19P GAIN WILD-TYPE   98   35
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               13                 98
  1               12                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED   14  1 15
  19P GAIN WILD-TYPE 77  7 78
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               14                 77
  M1                1                  7
  MX               15                 78
[1] 3 2
[1] 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               1                               35
  19P GAIN WILD-TYPE             4                              162
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19P GAIN MUTATED                                               1
  19P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19P GAIN MUTATED                                     2
  19P GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19P GAIN MUTATED                                           0
  19P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19P GAIN MUTATED                                              0
  19P GAIN WILD-TYPE                                            6
D34V6, multiclass
                                               clus
vv                                              19P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            35
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              19P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             162
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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  32
  19P GAIN WILD-TYPE  23 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   32
  19P GAIN WILD-TYPE   23  176
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 7                 23
  YES               32                176
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     4
  19P GAIN WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED                           5
  19P GAIN WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           0    26
  19P GAIN WILD-TYPE                                         1   143
D34V10, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                5                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   26                143
[1] 5 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  25
  19P GAIN WILD-TYPE  15 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   25
  19P GAIN WILD-TYPE   15  124
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               25                124
[1] 2 2
[1] FALSE
D34V12, continuous
D34V13, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   11  4
  19P GAIN WILD-TYPE 60 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     11    4
  19P GAIN WILD-TYPE   60   21
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  TUMOR FREE               11                 60
  WITH TUMOR                4                 21
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  19P GAIN MUTATED        4      2       0      0       2            27       4
  19P GAIN WILD-TYPE     19      3       1     10       5           151      10
D34V14, multiclass
               clus
vv              19P GAIN MUTATED 19P GAIN WILD-TYPE
  BRAZIL                       4                 19
  CANADA                       2                  3
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      2                  5
  UNITED STATES               27                151
  VIETNAM                      4                 10
[1] 7 2
[1] 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    2 18 18  0  1
  19P GAIN WILD-TYPE 15 88 79  1 13
D34V15, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  G1                2                 15
  G2               18                 88
  G3               18                 79
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V16, continuous
D34V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19P GAIN MUTATED                                             7
  19P GAIN WILD-TYPE                                          24
                    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                                                 2
  19P GAIN WILD-TYPE                                               0
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19P GAIN MUTATED                2                  20
  19P GAIN WILD-TYPE             50                  92
D34V18, multiclass
                                                 clus
vv                                                19P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                 2
  LIFELONG NON-SMOKER                                           20
                                                 clus
vv                                                19P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  0
  CURRENT SMOKER                                                  50
  LIFELONG NON-SMOKER                                             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"
D34V19, continuous
D34V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  19P GAIN MUTATED             4       16             3        1
  19P GAIN WILD-TYPE          15       59             9       11
D34V21, multiclass
               clus
vv              19P GAIN MUTATED 19P GAIN WILD-TYPE
  COMBINATION                  4                 15
  EXTERNAL                    16                 59
  EXTERNAL BEAM                3                  9
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V22, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    5  1
  19P GAIN WILD-TYPE 20  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      5    1
  19P GAIN WILD-TYPE   20    2
                         clus
vv                        19P GAIN MUTATED 19P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   5                 20
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  19P GAIN MUTATED                    0                1                   8
  19P GAIN WILD-TYPE                  2                1                  20
                    vv
clus                 REGIONAL SITE
  19P GAIN MUTATED               2
  19P GAIN WILD-TYPE            14
D34V23, multiclass
                     clus
vv                    19P GAIN MUTATED 19P GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   1                  1
  PRIMARY TUMOR FIELD                8                 20
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V24, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    8  1
  19P GAIN WILD-TYPE 26  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      8    1
  19P GAIN WILD-TYPE   26    2
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  CGY                8                 26
  GY                 1                  2
[1] 2 2
[1] FALSE
D34V25, continuous
D34V26, continuous
D34V27, continuous
D34V28, continuous
D34V29, continuous
D34V30, 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                         4                       0
  19P GAIN WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19P GAIN MUTATED                         1
  19P GAIN WILD-TYPE                       6
D34V31, multiclass
                                     clus
vv                                    19P GAIN MUTATED 19P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            4                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             14
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19P GAIN MUTATED                                                                                  11
  19P GAIN WILD-TYPE                                                                                57
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19P GAIN MUTATED                                                                                             18
  19P GAIN WILD-TYPE                                                                                           87
D34V32, 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)                          11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               18
                                                                                              clus
vv                                                                                             19P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V33, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    7 15
  19P GAIN WILD-TYPE 61 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   15
  19P GAIN WILD-TYPE   61   55
         clus
vv        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ABSENT                 7                 61
  PRESENT               15                 55
[1] 2 2
[1] FALSE
D34V34, continuous
D34V35, continuous
D34V36, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   11 11
  19P GAIN WILD-TYPE 32 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     11   11
  19P GAIN WILD-TYPE   32   83
                                          clus
vv                                         19P GAIN MUTATED 19P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   11                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               11                 83
[1] 2 2
[1] FALSE
D34V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19P GAIN MUTATED              1           8         12
  19P GAIN WILD-TYPE            9          41         45
D34V38, multiclass
              clus
vv             19P GAIN MUTATED 19P GAIN WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 8                 41
  NEVER USED                 12                 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"
D34V39, continuous
D34V40, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   13  0
  19P GAIN WILD-TYPE 76 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13    0
  19P GAIN WILD-TYPE   76   16
         clus
vv        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ABSENT                13                 76
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D34V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  19P GAIN MUTATED     0    0   3    7    3  2   2    1    1   4  1   4  0   1
  19P GAIN WILD-TYPE   1    1  27   58   21  2   6    6    8  18  0   4  2   0
                    vv
clus                 TX
  19P GAIN MUTATED    2
  19P GAIN WILD-TYPE 12
D34V42, multiclass
      clus
vv     19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 3                 27
  T1B1                7                 58
  T1B2                3                 21
  T2                  2                  2
  T2A                 2                  6
  T2A1                1                  6
  T2A2                1                  8
  T2B                 4                 18
  T3                  1                  0
  T3B                 4                  4
  T4                  0                  2
  TIS                 1                  0
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  19P GAIN MUTATED         0        0         0         0        4         5
  19P GAIN WILD-TYPE       4        2         1         1       27        64
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  19P GAIN MUTATED           5        1         2          0          2
  19P GAIN WILD-TYPE        27        2         4          5          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  19P GAIN MUTATED           7         1          8         1         1
  19P GAIN WILD-TYPE        20         0         26         2         6
D34V44, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 27
  STAGE IB1                 5                 64
  STAGE IB2                 5                 27
  STAGE II                  1                  2
  STAGE IIA                 2                  4
  STAGE IIA1                0                  5
  STAGE IIA2                2                  5
  STAGE IIB                 7                 20
  STAGE III                 1                  0
  STAGE IIIB                8                 26
  STAGE IVA                 1                  2
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    44  13
  19Q GAIN WILD-TYPE 139  37
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                176 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                13                 37 
$`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-C5-A8XH TCGA-C5-A8YR 
      154.32       134.33       147.35         9.34        45.83        27.52 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WI 
        4.47        58.88        44.94         2.66        22.98         8.28 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZF 
       14.50         1.35        14.50         1.81        13.91        14.96 
TCGA-EA-A97N TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RJ 
        0.36         0.43         0.59         0.59        16.08         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        2.24         0.10         1.35         7.13        21.67        20.78 
TCGA-IR-A3LL TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BE TCGA-PN-A8MA 
       36.36       195.85         0.30         0.20         0.07         2.96 
TCGA-Q1-A5R3 TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A954 
       15.95        12.16        14.07        49.55        16.64        42.58 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       43.82        39.35        38.96 

$`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-A1ML TCGA-C5-A1MN 
       46.32        30.21        35.01         0.46        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
        3.58        44.22        73.45        83.05       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL 
        0.82        18.02        17.85        20.42       101.82        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
       20.35        17.19        85.55        60.69        94.95        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99         8.35        75.78        99.91        23.51 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL 
        6.12        20.91         1.12        50.76        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88        36.76       117.99       118.65        16.83        16.18 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA 
        0.62        13.05         1.18         1.35        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        15.02        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45         0.13         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
       23.70         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-EX-A8YF 
        7.92         6.94        14.70        19.79         6.12         4.73 
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-GH-A9DA TCGA-HG-A2PA TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.97         1.12         9.01        25.41        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        10.06         5.13         6.71        21.11 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       30.31         7.99        11.28         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       13.87         0.03         5.42        29.72         4.34         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        13.35         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         5.88         6.25        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        93.99        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       20.22        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       11.51        39.78        31.27         4.73        23.24        44.88 
TCGA-VS-A957 TCGA-WL-A834 
       42.08        18.05 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.07               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            195.85             177.04 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             15.95              15.73 
[1] "0.1 - 195.8 (15.9)" "0.0 - 177.0 (15.7)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 T1 T2 T3+T4
  19Q GAIN MUTATED   23 15     5
  19Q GAIN WILD-TYPE 98 35     6
D35V3, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                  23                 98
  T2                  15                 35
  T3+T4                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   24 12
  19Q GAIN WILD-TYPE 87 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24   12
  19Q GAIN WILD-TYPE   87   35
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               24                 87
  1               12                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED   23  0 22
  19Q GAIN WILD-TYPE 68  8 71
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               23                 68
  M1                0                  8
  MX               22                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED               1                               53
  19Q GAIN WILD-TYPE             4                              144
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19Q GAIN MUTATED                                               1
  19Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19Q GAIN MUTATED                                     3
  19Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19Q GAIN MUTATED                                           0
  19Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19Q GAIN MUTATED                                              0
  19Q GAIN WILD-TYPE                                            6
D35V6, multiclass
                                               clus
vv                                              19Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            53
  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                                              19Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             144
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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    12  46
  19Q GAIN WILD-TYPE  18 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     12   46
  19Q GAIN WILD-TYPE   18  162
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                12                 18
  YES               46                162
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     4
  19Q GAIN WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED                           6
  19Q GAIN WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           0    42
  19Q GAIN WILD-TYPE                                         1   127
D35V10, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                6                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   42                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"
D35V11, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  40
  19Q GAIN WILD-TYPE  15 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   40
  19Q GAIN WILD-TYPE   15  109
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               40                109
[1] 2 2
[1] FALSE
D35V12, continuous
D35V13, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   16  9
  19Q GAIN WILD-TYPE 55 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     16    9
  19Q GAIN WILD-TYPE   55   16
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  TUMOR FREE               16                 55
  WITH TUMOR                9                 16
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  19Q GAIN MUTATED        7      2       1      1       4            39       4
  19Q GAIN WILD-TYPE     16      3       0      9       3           139      10
D35V14, multiclass
               clus
vv              19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  BRAZIL                       7                 16
  CANADA                       2                  3
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      4                  3
  UNITED STATES               39                139
  VIETNAM                      4                 10
[1] 7 2
[1] 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    3 25 27  0  1
  19Q GAIN WILD-TYPE 14 81 70  1 13
D35V15, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  G1                3                 14
  G2               25                 81
  G3               27                 70
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V16, continuous
D35V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19Q GAIN MUTATED                                             9
  19Q GAIN WILD-TYPE                                          22
                    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                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19Q GAIN MUTATED                5                  29
  19Q GAIN WILD-TYPE             47                  83
D35V18, multiclass
                                                 clus
vv                                                19Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 5
  LIFELONG NON-SMOKER                                           29
                                                 clus
vv                                                19Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  47
  LIFELONG NON-SMOKER                                             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"
D35V19, continuous
D35V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  19Q GAIN MUTATED             7       17             5        3
  19Q GAIN WILD-TYPE          12       58             7        9
D35V21, multiclass
               clus
vv              19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COMBINATION                  7                 12
  EXTERNAL                    17                 58
  EXTERNAL BEAM                5                  7
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V22, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    9  2
  19Q GAIN WILD-TYPE 16  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9    2
  19Q GAIN WILD-TYPE   16    1
                         clus
vv                        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  19Q GAIN MUTATED                    0                2                   7
  19Q GAIN WILD-TYPE                  2                0                  21
                    vv
clus                 REGIONAL SITE
  19Q GAIN MUTATED               6
  19Q GAIN WILD-TYPE            10
D35V23, multiclass
                     clus
vv                    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   2                  0
  PRIMARY TUMOR FIELD                7                 21
  REGIONAL SITE                      6                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V24, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   13  0
  19Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13    0
  19Q GAIN WILD-TYPE   21    3
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CGY               13                 21
  GY                 0                  3
[1] 2 2
[1] FALSE
D35V25, continuous
D35V26, continuous
D35V27, continuous
D35V28, continuous
D35V29, continuous
D35V30, 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                         7                       0
  19Q GAIN WILD-TYPE                      22                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19Q GAIN MUTATED                         1
  19Q GAIN WILD-TYPE                       6
D35V31, multiclass
                                     clus
vv                                    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                            7                 22
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  19Q GAIN MUTATED                                               0
  19Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  19Q GAIN MUTATED                                                3
  19Q GAIN WILD-TYPE                                             13
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19Q GAIN MUTATED                                                                                  15
  19Q GAIN WILD-TYPE                                                                                53
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19Q GAIN MUTATED                                                                                             24
  19Q GAIN WILD-TYPE                                                                                           81
D35V32, multiclass
                                                                                              clus
vv                                                                                             19Q 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)                          15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               24
                                                                                              clus
vv                                                                                             19Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V33, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   12 20
  19Q GAIN WILD-TYPE 56 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     12   20
  19Q GAIN WILD-TYPE   56   50
         clus
vv        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ABSENT                12                 56
  PRESENT               20                 50
[1] 2 2
[1] FALSE
D35V34, continuous
D35V35, continuous
D35V36, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   14 22
  19Q GAIN WILD-TYPE 29 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     14   22
  19Q GAIN WILD-TYPE   29   72
                                          clus
vv                                         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   14                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               22                 72
[1] 2 2
[1] FALSE
D35V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19Q GAIN MUTATED              2          11         17
  19Q GAIN WILD-TYPE            8          38         40
D35V38, multiclass
              clus
vv             19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                11                 38
  NEVER USED                 17                 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"
D35V39, continuous
D35V40, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   18  3
  19Q GAIN WILD-TYPE 71 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     18    3
  19Q GAIN WILD-TYPE   71   13
         clus
vv        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ABSENT                18                 71
  PRESENT                3                 13
[1] 2 2
[1] FALSE
D35V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  19Q GAIN MUTATED     0    0   6   13    4  1   2    2    2   8  1   4  0   0
  19Q GAIN WILD-TYPE   1    1  24   52   20  3   6    5    7  14  0   4  2   1
                    vv
clus                 TX
  19Q GAIN MUTATED    2
  19Q GAIN WILD-TYPE 12
D35V42, multiclass
      clus
vv     19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 6                 24
  T1B1               13                 52
  T1B2                4                 20
  T2                  1                  3
  T2A                 2                  6
  T2A1                2                  5
  T2A2                2                  7
  T2B                 8                 14
  T3                  1                  0
  T3B                 4                  4
  T4                  0                  2
  TIS                 0                  1
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  19Q GAIN MUTATED         0        0         0         0        7        13
  19Q GAIN WILD-TYPE       4        2         1         1       24        56
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  19Q GAIN MUTATED           8        1         1          1          3
  19Q GAIN WILD-TYPE        24        2         5          4          4
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  19Q GAIN MUTATED          11         1         10         1         0
  19Q GAIN WILD-TYPE        16         0         24         2         7
D35V44, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  7                 24
  STAGE IB1                13                 56
  STAGE IB2                 8                 24
  STAGE II                  1                  2
  STAGE IIA                 1                  5
  STAGE IIA1                1                  4
  STAGE IIA2                3                  4
  STAGE IIB                11                 16
  STAGE III                 1                  0
  STAGE IIIB               10                 24
  STAGE IVA                 1                  2
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    63  17
  20P GAIN WILD-TYPE 120  33
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                80                153 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                17                 33 
$`20P GAIN MUTATED`
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI 
      144.16       173.29        67.46        31.40        35.01        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LZ 
        0.46        40.93         3.58        73.18        73.45       100.14 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
      182.93       154.32        20.35       147.35        17.19        60.69 
TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DS-A0VK 
        2.73        27.52         1.12        58.88        40.04        36.76 
TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3QD 
       22.98        17.52         0.76         1.74         0.82        13.05 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N 
       14.50        14.89         1.48        14.96        13.58         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
       12.59        26.27         1.51         0.59         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       16.08         1.18         2.24         1.22        23.84         2.17 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LF 
        1.45         1.35        21.67        20.78       147.39        96.95 
TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q0 TCGA-LP-A4AX TCGA-LP-A7HU TCGA-PN-A8MA 
       20.48        10.06       195.85         0.07         0.20         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73S 
       15.58        13.35        15.95         3.39        17.56        10.39 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EI 
        3.88        93.99        12.16        61.28        34.52        14.07 
TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A954 
       19.96        23.28        11.51        31.27        16.64        42.58 
TCGA-VS-A959 TCGA-WL-A834 
       39.35        18.05 

$`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-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML 
       30.21        57.73        53.16        38.99         2.43        20.91 
TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       44.22        83.05        78.35        38.43         0.82        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       18.02        17.85        20.42       101.82       134.33        15.48 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
       85.55        94.95         9.34        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35        75.78        99.91        23.51         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
        4.47        50.76        44.94        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT 
      117.99       118.65        16.83        16.18         8.28        12.36 
TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        1.32         0.62         1.18        14.50         1.35         1.35 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD 
        1.81        12.66        12.82         0.26        13.91        15.02 
TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R8 
       14.99        13.48        45.96         6.64         0.43         1.45 
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-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-EX-A8YF TCGA-FU-A2QG 
        6.94        14.70        19.79         6.12         4.73         0.92 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
       14.93         9.44       137.16        66.81       117.40        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 
       21.44        15.58         5.13         6.71        21.11        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y 
        7.99        11.28         0.89         0.30         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
        0.03         5.42        29.72         0.07         4.34         5.49 
TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
       16.14        14.07        15.88         5.88         6.25        19.59 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 
       11.67        10.03        29.03        20.22        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       46.03        49.55        39.78         4.73        23.24        44.88 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 
       42.08        43.82        38.96 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            195.85             177.04 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            16.915             15.020 
[1] "0.1 - 195.8 (16.9)" "0.0 - 177.0 (15.0)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 T1 T2 T3+T4
  20P GAIN MUTATED   40 13     7
  20P GAIN WILD-TYPE 81 37     4
D36V3, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                  40                 81
  T2                  13                 37
  T3+T4                7                  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"
D36V4, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   29 22
  20P GAIN WILD-TYPE 82 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     29   22
  20P GAIN WILD-TYPE   82   25
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               29                 82
  1               22                 25
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   33  2 29
  20P GAIN WILD-TYPE 58  6 64
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               33                 58
  M1                2                  6
  MX               29                 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
  20P GAIN MUTATED               2                               65
  20P GAIN WILD-TYPE             3                              132
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20P GAIN MUTATED                                               2
  20P GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20P GAIN MUTATED                                     8
  20P GAIN WILD-TYPE                                  14
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20P GAIN MUTATED                                           2
  20P GAIN WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20P GAIN MUTATED                                              2
  20P GAIN WILD-TYPE                                            4
D36V6, multiclass
                                               clus
vv                                              20P GAIN MUTATED
  ADENOSQUAMOUS                                                2
  CERVICAL SQUAMOUS CELL CARCINOMA                            65
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              20P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  3
  CERVICAL SQUAMOUS CELL CARCINOMA                             132
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           14
  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"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    10  71
  20P GAIN WILD-TYPE  20 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10   71
  20P GAIN WILD-TYPE   20  137
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                10                 20
  YES               71                137
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     5
  20P GAIN WILD-TYPE                                8    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED                           9
  20P GAIN WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           0    57
  20P GAIN WILD-TYPE                                         1   112
D36V10, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    5                 13
  BLACK OR AFRICAN AMERICAN                                9                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   57                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"
D36V11, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    4 51
  20P GAIN WILD-TYPE 12 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   51
  20P GAIN WILD-TYPE   12   98
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               51                 98
[1] 2 2
[1] FALSE
D36V12, continuous
D36V13, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   23 10
  20P GAIN WILD-TYPE 48 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     23   10
  20P GAIN WILD-TYPE   48   15
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  TUMOR FREE               23                 48
  WITH TUMOR               10                 15
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  20P GAIN MUTATED        9      3       1      4       2            57       5
  20P GAIN WILD-TYPE     14      2       0      6       5           121       9
D36V14, multiclass
               clus
vv              20P GAIN MUTATED 20P GAIN WILD-TYPE
  BRAZIL                       9                 14
  CANADA                       3                  2
  NIGERIA                      1                  0
  RUSSIA                       4                  6
  UKRAINE                      2                  5
  UNITED STATES               57                121
  VIETNAM                      5                  9
[1] 7 2
[1] 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    3 33 37  0  8
  20P GAIN WILD-TYPE 14 73 60  1  6
D36V15, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  G1                3                 14
  G2               33                 73
  G3               37                 60
  G4                0                  1
  GX                8                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V16, continuous
D36V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20P GAIN MUTATED                                            13
  20P GAIN WILD-TYPE                                          18
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20P GAIN MUTATED               13                  39
  20P GAIN WILD-TYPE             39                  73
D36V18, multiclass
                                                 clus
vv                                                20P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                13
  LIFELONG NON-SMOKER                                           39
                                                 clus
vv                                                20P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  39
  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"
D36V19, continuous
D36V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  20P GAIN MUTATED             6       26             6        4
  20P GAIN WILD-TYPE          13       49             6        8
D36V21, multiclass
               clus
vv              20P GAIN MUTATED 20P GAIN WILD-TYPE
  COMBINATION                  6                 13
  EXTERNAL                    26                 49
  EXTERNAL BEAM                6                  6
  INTERNAL                     4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V22, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    9  0
  20P GAIN WILD-TYPE 16  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9    0
  20P GAIN WILD-TYPE   16    3
                         clus
vv                        20P GAIN MUTATED 20P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  20P GAIN MUTATED                    0                1                   6
  20P GAIN WILD-TYPE                  2                1                  22
                    vv
clus                 REGIONAL SITE
  20P GAIN MUTATED               7
  20P GAIN WILD-TYPE             9
D36V23, multiclass
                     clus
vv                    20P GAIN MUTATED 20P GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   1                  1
  PRIMARY TUMOR FIELD                6                 22
  REGIONAL SITE                      7                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V24, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   12  0
  20P GAIN WILD-TYPE 22  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12    0
  20P GAIN WILD-TYPE   22    3
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  CGY               12                 22
  GY                 0                  3
[1] 2 2
[1] FALSE
D36V25, continuous
D36V26, continuous
D36V27, continuous
D36V28, continuous
D36V29, continuous
D36V30, 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                         9                       0
  20P GAIN WILD-TYPE                      20                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20P GAIN MUTATED                         3
  20P GAIN WILD-TYPE                       4
D36V31, multiclass
                                     clus
vv                                    20P GAIN MUTATED 20P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            9                 20
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  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)
  20P GAIN MUTATED                                               1
  20P GAIN WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  20P GAIN MUTATED                                                7
  20P GAIN WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20P GAIN MUTATED                                                                                  24
  20P GAIN WILD-TYPE                                                                                44
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20P GAIN MUTATED                                                                                             34
  20P GAIN WILD-TYPE                                                                                           71
D36V32, multiclass
                                                                                              clus
vv                                                                                             20P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          24
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               34
                                                                                              clus
vv                                                                                             20P 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)                 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"
D36V33, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   21 25
  20P GAIN WILD-TYPE 47 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     21   25
  20P GAIN WILD-TYPE   47   45
         clus
vv        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ABSENT                21                 47
  PRESENT               25                 45
[1] 2 2
[1] FALSE
D36V34, continuous
D36V35, continuous
D36V36, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   11 32
  20P GAIN WILD-TYPE 32 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     11   32
  20P GAIN WILD-TYPE   32   62
                                          clus
vv                                         20P GAIN MUTATED 20P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   11                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               32                 62
[1] 2 2
[1] FALSE
D36V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20P GAIN MUTATED              3          19         18
  20P GAIN WILD-TYPE            7          30         39
D36V38, multiclass
              clus
vv             20P GAIN MUTATED 20P GAIN WILD-TYPE
  CURRENT USER                3                  7
  FORMER USER                19                 30
  NEVER USED                 18                 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"
D36V39, continuous
D36V40, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   29  5
  20P GAIN WILD-TYPE 60 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     29    5
  20P GAIN WILD-TYPE   60   11
         clus
vv        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ABSENT                29                 60
  PRESENT                5                 11
[1] 2 2
[1] FALSE
D36V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  20P GAIN MUTATED     0    0   9   26    5  1   2    3    1   6  1   6  0   0
  20P GAIN WILD-TYPE   1    1  21   39   19  3   6    4    8  16  0   2  2   1
                    vv
clus                 TX
  20P GAIN MUTATED    6
  20P GAIN WILD-TYPE  8
D36V42, multiclass
      clus
vv     20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 9                 21
  T1B1               26                 39
  T1B2                5                 19
  T2                  1                  3
  T2A                 2                  6
  T2A1                3                  4
  T2A2                1                  8
  T2B                 6                 16
  T3                  1                  0
  T3B                 6                  2
  T4                  0                  2
  TIS                 0                  1
  TX                  6                  8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  20P GAIN MUTATED         2        0         0         0       11        22
  20P GAIN WILD-TYPE       2        2         1         1       20        47
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  20P GAIN MUTATED           8        2         1          2          2
  20P GAIN WILD-TYPE        24        1         5          3          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  20P GAIN MUTATED          11         1         13         1         1
  20P GAIN WILD-TYPE        16         0         21         2         6
D36V44, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                 11                 20
  STAGE IB1                22                 47
  STAGE IB2                 8                 24
  STAGE II                  2                  1
  STAGE IIA                 1                  5
  STAGE IIA1                2                  3
  STAGE IIA2                2                  5
  STAGE IIB                11                 16
  STAGE III                 1                  0
  STAGE IIIB               13                 21
  STAGE IVA                 1                  2
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    74  18
  20Q GAIN WILD-TYPE 109  32
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                92                141 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                18                 32 
$`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       154.32        20.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ 
       60.69         2.73        75.78        27.52         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT 
       50.76        40.04        22.98        17.52         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-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.96        13.58         0.36        12.59        45.96        26.27 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RJ 
        1.51         0.59         0.59         0.13        16.08         1.18 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
        0.10         0.03         1.22        23.84         2.17         0.66 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 
        1.45         1.35         9.01        21.67        20.78       147.39 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q0 
       96.95        78.71        20.48        10.06        21.11       195.85 
TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        0.07         0.20         5.49         2.96        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 
       15.95         3.39        17.56        15.88        10.39         3.88 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ 
       93.99        12.16        61.28        34.52        14.07        19.96 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A954 
       23.28        11.51        39.78        31.27        16.64        42.58 
TCGA-VS-A959 TCGA-WL-A834 
       39.35        18.05 

$`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-A1ML TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       53.16        38.99        20.91        44.22        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE 
       20.42       101.82       134.33        15.48       147.35        85.55 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34        13.61        50.99        45.83         8.35 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KL 
       99.91        23.51         6.12        20.91         4.47        44.94 
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-A7WI TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       16.83        16.18         8.28         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-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EK-A2IP 
        0.26        13.91        15.02        14.99        13.48         6.64 
TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.43         1.45         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-EX-A8YF 
        7.92         6.94        14.70        19.79         6.12         4.73 
TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.92         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41         7.13        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK 
        9.44       137.16        66.81       117.40        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        5.13         6.71        30.31         7.99        11.28         0.89 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.30         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R 
        0.07         4.34        16.14        14.07         5.88         6.25 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL 
       19.59        11.67        10.03        29.03        20.22        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       32.15        46.03        49.55         4.73        23.24        44.88 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 
       42.08        43.82        38.96 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.03               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            195.85             177.04 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             16.36              15.02 
[1] "0.0 - 195.8 (16.4)" "0.0 - 177.0 (15.0)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 T1 T2 T3+T4
  20Q GAIN MUTATED   46 16     7
  20Q GAIN WILD-TYPE 75 34     4
D37V3, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                  46                 75
  T2                  16                 34
  T3+T4                7                  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"
D37V4, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   39 22
  20Q GAIN WILD-TYPE 72 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     39   22
  20Q GAIN WILD-TYPE   72   25
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               39                 72
  1               22                 25
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   39  3 33
  20Q GAIN WILD-TYPE 52  5 60
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               39                 52
  M1                3                  5
  MX               33                 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
  20Q GAIN MUTATED               2                               74
  20Q GAIN WILD-TYPE             3                              123
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20Q GAIN MUTATED                                               2
  20Q GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20Q GAIN MUTATED                                    11
  20Q GAIN WILD-TYPE                                  11
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20Q GAIN MUTATED                                           2
  20Q GAIN WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20Q GAIN MUTATED                                              3
  20Q GAIN WILD-TYPE                                            3
D37V6, multiclass
                                               clus
vv                                              20Q GAIN MUTATED
  ADENOSQUAMOUS                                                2
  CERVICAL SQUAMOUS CELL CARCINOMA                            74
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 3
                                               clus
vv                                              20Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  3
  CERVICAL SQUAMOUS CELL CARCINOMA                             123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           11
  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"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    12  82
  20Q GAIN WILD-TYPE  18 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     12   82
  20Q GAIN WILD-TYPE   18  126
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                12                 18
  YES               82                126
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     6
  20Q GAIN WILD-TYPE                                8    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED                          10
  20Q GAIN WILD-TYPE                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           0    67
  20Q GAIN WILD-TYPE                                         1   102
D37V10, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    6                 12
  BLACK OR AFRICAN AMERICAN                               10                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   67                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"
D37V11, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5 58
  20Q GAIN WILD-TYPE 11 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5   58
  20Q GAIN WILD-TYPE   11   91
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO               58                 91
[1] 2 2
[1] FALSE
D37V12, continuous
D37V13, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   27 10
  20Q GAIN WILD-TYPE 44 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     27   10
  20Q GAIN WILD-TYPE   44   15
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  TUMOR FREE               27                 44
  WITH TUMOR               10                 15
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  20Q GAIN MUTATED       10      4       1      6       2            65       6
  20Q GAIN WILD-TYPE     13      1       0      4       5           113       8
D37V14, multiclass
               clus
vv              20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  BRAZIL                      10                 13
  CANADA                       4                  1
  NIGERIA                      1                  0
  RUSSIA                       6                  4
  UKRAINE                      2                  5
  UNITED STATES               65                113
  VIETNAM                      6                  8
[1] 7 2
[1] 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    5 37 42  1  8
  20Q GAIN WILD-TYPE 12 69 55  0  6
D37V15, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  G1                5                 12
  G2               37                 69
  G3               42                 55
  G4                1                  0
  GX                8                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V16, continuous
D37V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20Q GAIN MUTATED                                            16
  20Q GAIN WILD-TYPE                                          15
                    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                                                 1
  20Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20Q GAIN MUTATED               15                  45
  20Q GAIN WILD-TYPE             37                  67
D37V18, multiclass
                                                 clus
vv                                                20Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                15
  LIFELONG NON-SMOKER                                           45
                                                 clus
vv                                                20Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  37
  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"
D37V19, continuous
D37V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  20Q GAIN MUTATED             6       29             6        4
  20Q GAIN WILD-TYPE          13       46             6        8
D37V21, multiclass
               clus
vv              20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COMBINATION                  6                 13
  EXTERNAL                    29                 46
  EXTERNAL BEAM                6                  6
  INTERNAL                     4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V22, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    9  2
  20Q GAIN WILD-TYPE 16  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      9    2
  20Q GAIN WILD-TYPE   16    1
                         clus
vv                        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  20Q GAIN MUTATED                    0                1                  10
  20Q GAIN WILD-TYPE                  2                1                  18
                    vv
clus                 REGIONAL SITE
  20Q GAIN MUTATED               6
  20Q GAIN WILD-TYPE            10
D37V23, multiclass
                     clus
vv                    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   1                  1
  PRIMARY TUMOR FIELD               10                 18
  REGIONAL SITE                      6                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V24, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   13  1
  20Q GAIN WILD-TYPE 21  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     13    1
  20Q GAIN WILD-TYPE   21    2
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CGY               13                 21
  GY                 1                  2
[1] 2 2
[1] FALSE
D37V25, continuous
D37V26, continuous
D37V27, continuous
D37V28, continuous
D37V29, continuous
D37V30, 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                         8                       0
  20Q GAIN WILD-TYPE                      21                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20Q GAIN MUTATED                         3
  20Q GAIN WILD-TYPE                       4
D37V31, multiclass
                                     clus
vv                                    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            8                 21
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  20Q GAIN MUTATED                                               0
  20Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  20Q GAIN MUTATED                                                7
  20Q GAIN WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20Q GAIN MUTATED                                                                                  28
  20Q GAIN WILD-TYPE                                                                                40
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20Q GAIN MUTATED                                                                                             40
  20Q GAIN WILD-TYPE                                                                                           65
D37V32, multiclass
                                                                                              clus
vv                                                                                             20Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               40
                                                                                              clus
vv                                                                                             20Q 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)                 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"
D37V33, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   28 26
  20Q GAIN WILD-TYPE 40 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     28   26
  20Q GAIN WILD-TYPE   40   44
         clus
vv        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ABSENT                28                 40
  PRESENT               26                 44
[1] 2 2
[1] FALSE
D37V34, continuous
D37V35, continuous
D37V36, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   11 37
  20Q GAIN WILD-TYPE 32 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11   37
  20Q GAIN WILD-TYPE   32   57
                                          clus
vv                                         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   11                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               37                 57
[1] 2 2
[1] FALSE
D37V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20Q GAIN MUTATED              4          22         19
  20Q GAIN WILD-TYPE            6          27         38
D37V38, multiclass
              clus
vv             20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CURRENT USER                4                  6
  FORMER USER                22                 27
  NEVER USED                 19                 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"
D37V39, continuous
D37V40, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   36  6
  20Q GAIN WILD-TYPE 53 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     36    6
  20Q GAIN WILD-TYPE   53   10
         clus
vv        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ABSENT                36                 53
  PRESENT                6                 10
[1] 2 2
[1] FALSE
D37V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  20Q GAIN MUTATED     0    0  12   28    6  1   3    4    1   7  1   6  0   1
  20Q GAIN WILD-TYPE   1    1  18   37   18  3   5    3    8  15  0   2  2   0
                    vv
clus                 TX
  20Q GAIN MUTATED    8
  20Q GAIN WILD-TYPE  6
D37V42, multiclass
      clus
vv     20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                12                 18
  T1B1               28                 37
  T1B2                6                 18
  T2                  1                  3
  T2A                 3                  5
  T2A1                4                  3
  T2A2                1                  8
  T2B                 7                 15
  T3                  1                  0
  T3B                 6                  2
  T4                  0                  2
  TIS                 1                  0
  TX                  8                  6
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  20Q GAIN MUTATED         2        0         0         0       12        27
  20Q GAIN WILD-TYPE       2        2         1         1       19        42
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  20Q GAIN MUTATED           8        3         2          3          2
  20Q GAIN WILD-TYPE        24        0         4          2          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  20Q GAIN MUTATED          12         1         16         1         1
  20Q GAIN WILD-TYPE        15         0         18         2         6
D37V44, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                 12                 19
  STAGE IB1                27                 42
  STAGE IB2                 8                 24
  STAGE II                  3                  0
  STAGE IIA                 2                  4
  STAGE IIA1                3                  2
  STAGE IIA2                2                  5
  STAGE IIB                12                 15
  STAGE III                 1                  0
  STAGE IIIB               16                 18
  STAGE IVA                 1                  2
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    21   8
  21Q GAIN WILD-TYPE 162  42
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                29                204 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                 42 
$`21Q GAIN MUTATED`
TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP 
       19.86        31.40        38.99        35.61         2.43         3.58 
TCGA-C5-A2LZ TCGA-C5-A7X8 TCGA-DG-A2KH TCGA-DG-A2KL TCGA-EA-A1QS TCGA-EA-A3HQ 
      100.14         2.73         1.12        44.94         0.76         1.74 
TCGA-EA-A5O9 TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RM TCGA-FU-A3TX TCGA-HM-A3JK 
       13.91         0.59        16.08         2.24         1.48        20.78 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A5U2 
       36.36        21.44        21.11        30.31        11.28         0.30 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QF 
        0.07         5.49        19.96        23.28        49.55 

$`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-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
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-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        0.46        20.91        40.93        44.22        73.18        73.45 
TCGA-C5-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-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       182.93       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        4.47        58.88        50.76        40.04        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-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52         8.28        12.36         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-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
        1.48        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
        0.36        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC 
        0.43         0.59         1.45         0.13         0.07         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         6.12         4.73         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-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
        9.01        25.41         7.13        21.67        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        26.56        27.42         3.29        24.56        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58        10.06         5.13         6.71       195.85         7.99 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.89         0.07         0.82         0.20        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        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC 
       20.22        14.07        53.52        32.15        46.03        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        16.64         4.73        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            100.14             195.85 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             16.08              15.73 
[1] "0.1 - 100.1 (16.1)" "0.0 - 195.8 (15.7)"
[1] "hr=" "1.9"
D38V2, continuous
                    vv
clus                  T1  T2 T3+T4
  21Q GAIN MUTATED    12   9     0
  21Q GAIN WILD-TYPE 109  41    11
D38V3, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                  12                109
  T2                   9                 41
  T3+T4                0                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   14  6
  21Q GAIN WILD-TYPE 97 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     14    6
  21Q GAIN WILD-TYPE   97   41
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               14                 97
  1                6                 41
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  21Q GAIN MUTATED   11  2 10
  21Q GAIN WILD-TYPE 80  6 83
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               11                 80
  M1                2                  6
  MX               10                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED               1                               27
  21Q GAIN WILD-TYPE             4                              170
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  21Q GAIN MUTATED                                               1
  21Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  21Q GAIN MUTATED                                     1
  21Q GAIN WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  21Q GAIN MUTATED                                           0
  21Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  21Q GAIN MUTATED                                              1
  21Q GAIN WILD-TYPE                                            5
D38V6, multiclass
                                               clus
vv                                              21Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              21Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             170
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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     5  26
  21Q GAIN WILD-TYPE  25 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   26
  21Q GAIN WILD-TYPE   25  182
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 5                 25
  YES               26                182
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     3
  21Q GAIN WILD-TYPE                                7    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED                           3
  21Q GAIN WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    19
  21Q GAIN WILD-TYPE                                         1   150
D38V10, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                3                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   19                150
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3  17
  21Q GAIN WILD-TYPE  13 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   17
  21Q GAIN WILD-TYPE   13  132
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               17                132
[1] 2 2
[1] FALSE
D38V12, continuous
D38V13, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    8  7
  21Q GAIN WILD-TYPE 63 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8    7
  21Q GAIN WILD-TYPE   63   18
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  TUMOR FREE                8                 63
  WITH TUMOR                7                 18
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  21Q GAIN MUTATED        3      2       0      2       1            21       2
  21Q GAIN WILD-TYPE     20      3       1      8       6           157      12
D38V14, multiclass
               clus
vv              21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  BRAZIL                       3                 20
  CANADA                       2                  3
  NIGERIA                      0                  1
  RUSSIA                       2                  8
  UKRAINE                      1                  6
  UNITED STATES               21                157
  VIETNAM                      2                 12
[1] 7 2
[1] 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    1 11 17  0  2
  21Q GAIN WILD-TYPE 16 95 80  1 12
D38V15, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  G1                1                 16
  G2               11                 95
  G3               17                 80
  G4                0                  1
  GX                2                 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"
D38V16, continuous
D38V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  21Q GAIN MUTATED                                             6
  21Q GAIN WILD-TYPE                                          25
                    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                                                 1
  21Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  21Q GAIN MUTATED                4                  15
  21Q GAIN WILD-TYPE             48                  97
D38V18, multiclass
                                                 clus
vv                                                21Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                           15
                                                 clus
vv                                                21Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  48
  LIFELONG NON-SMOKER                                             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"
D38V19, continuous
D38V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  21Q GAIN MUTATED             4       10             1        1
  21Q GAIN WILD-TYPE          15       65            11       11
D38V21, multiclass
               clus
vv              21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COMBINATION                  4                 15
  EXTERNAL                    10                 65
  EXTERNAL BEAM                1                 11
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V22, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  1
  21Q GAIN WILD-TYPE 22  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    1
  21Q GAIN WILD-TYPE   22    2
                         clus
vv                        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   3                 22
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  21Q GAIN MUTATED                    0                0                   4
  21Q GAIN WILD-TYPE                  2                2                  24
                    vv
clus                 REGIONAL SITE
  21Q GAIN MUTATED               1
  21Q GAIN WILD-TYPE            15
D38V23, multiclass
                     clus
vv                    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                4                 24
  REGIONAL SITE                      1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V24, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  1
  21Q GAIN WILD-TYPE 32  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   32    2
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CGY                2                 32
  GY                 1                  2
[1] 2 2
[1] FALSE
D38V25, continuous
D38V26, continuous
D38V27, continuous
D38V28, continuous
D38V29, continuous
D38V30, 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                         2                       0
  21Q GAIN WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  21Q GAIN MUTATED                         2
  21Q GAIN WILD-TYPE                       5
D38V31, multiclass
                                     clus
vv                                    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            2                 27
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  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 GAIN MUTATED                                               0
  21Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  21Q GAIN MUTATED                                                2
  21Q GAIN WILD-TYPE                                             14
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  21Q GAIN MUTATED                                                                                  16
  21Q GAIN WILD-TYPE                                                                                52
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  21Q GAIN MUTATED                                                                                              9
  21Q GAIN WILD-TYPE                                                                                           96
D38V32, multiclass
                                                                                              clus
vv                                                                                             21Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                9
                                                                                              clus
vv                                                                                             21Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            52
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V33, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   10  8
  21Q GAIN WILD-TYPE 58 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    8
  21Q GAIN WILD-TYPE   58   62
         clus
vv        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ABSENT                10                 58
  PRESENT                8                 62
[1] 2 2
[1] FALSE
D38V34, continuous
D38V35, continuous
D38V36, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    8  6
  21Q GAIN WILD-TYPE 35 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8    6
  21Q GAIN WILD-TYPE   35   88
                                          clus
vv                                         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    8                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                6                 88
[1] 2 2
[1] FALSE
D38V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  21Q GAIN MUTATED              0           2          7
  21Q GAIN WILD-TYPE           10          47         50
D38V38, multiclass
              clus
vv             21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 2                 47
  NEVER USED                  7                 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"
D38V39, continuous
D38V40, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   10  1
  21Q GAIN WILD-TYPE 79 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    1
  21Q GAIN WILD-TYPE   79   15
         clus
vv        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ABSENT                10                 79
  PRESENT                1                 15
[1] 2 2
[1] FALSE
D38V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  21Q GAIN MUTATED     0    0   1    8    3  1   4    0    1   3  0   0  0   1
  21Q GAIN WILD-TYPE   1    1  29   57   21  3   4    7    8  19  1   8  2   0
                    vv
clus                 TX
  21Q GAIN MUTATED    1
  21Q GAIN WILD-TYPE 13
D38V42, multiclass
      clus
vv     21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 1                 29
  T1B1                8                 57
  T1B2                3                 21
  T2                  1                  3
  T2A                 4                  4
  T2A1                0                  7
  T2A2                1                  8
  T2B                 3                 19
  T3                  0                  1
  T3B                 0                  8
  T4                  0                  2
  TIS                 1                  0
  TX                  1                 13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  21Q GAIN MUTATED         0        0         0         1        2         8
  21Q GAIN WILD-TYPE       4        2         1         0       29        61
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  21Q GAIN MUTATED           3        1         2          0          2
  21Q GAIN WILD-TYPE        29        2         4          5          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  21Q GAIN MUTATED           5         0          7         0         0
  21Q GAIN WILD-TYPE        22         1         27         3         7
D38V44, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  2                 29
  STAGE IB1                 8                 61
  STAGE IB2                 3                 29
  STAGE II                  1                  2
  STAGE IIA                 2                  4
  STAGE IIA1                0                  5
  STAGE IIA2                2                  5
  STAGE IIB                 5                 22
  STAGE III                 0                  1
  STAGE IIIB                7                 27
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    22   3
  22Q GAIN WILD-TYPE 161  47
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                25                208 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 47 
$`22Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A1ML TCGA-C5-A2LY TCGA-C5-A7CG TCGA-C5-A7CH 
       57.04       144.16        20.91        78.35       182.93       154.32 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A8YQ TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A5ZF 
       17.19        60.69        23.51        22.98         0.76        14.96 
TCGA-EK-A2R9 TCGA-EK-A2RM TCGA-EK-A2RO TCGA-FU-A3NI TCGA-FU-A40J TCGA-JW-A5VI 
        0.13         2.24         0.07         1.45         1.35        24.56 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA 
       30.31        11.28         0.30        13.87         0.07         2.96 
TCGA-VS-A8QF 
       49.55 

$`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        20.35       147.35        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       75.78        99.91        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        58.88        50.76        44.94        40.04        87.75 
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-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18        17.52         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-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-A6QX 
       14.89         1.48        13.91        15.02        14.99        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.48         0.36        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA 
        1.51         0.43         0.59         0.59         1.45        16.08 
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-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         6.12         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
       23.84         0.92         2.17         0.66         1.02         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       21.11       195.85         7.99         0.89         0.07         0.82 
TCGA-LP-A7HU TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
        0.20         0.03         5.42        29.72         4.34         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
        3.88        11.67        93.99        12.16        61.28        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       34.52        29.03        20.22        14.07        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        46.03        23.28        11.51        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            182.93             195.85 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             17.19              15.73 
[1] "0.1 - 182.9 (17.2)" "0.0 - 195.8 (15.7)"
[1] "hr=" "2.1"
D39V2, continuous
                    vv
clus                  T1  T2 T3+T4
  22Q GAIN MUTATED    10   6     1
  22Q GAIN WILD-TYPE 111  44    10
D39V3, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                  10                111
  T2                   6                 44
  T3+T4                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10   5
  22Q GAIN WILD-TYPE 101  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10    5
  22Q GAIN WILD-TYPE  101   42
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               10                101
  1                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  22Q GAIN MUTATED    8  0  9
  22Q GAIN WILD-TYPE 83  8 84
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                8                 83
  M1                0                  8
  MX                9                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED               0                               23
  22Q GAIN WILD-TYPE             5                              174
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  22Q GAIN MUTATED                                               1
  22Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  22Q GAIN MUTATED                                     2
  22Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  22Q GAIN MUTATED                                           0
  22Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  22Q GAIN MUTATED                                              0
  22Q GAIN WILD-TYPE                                            6
D39V6, multiclass
                                               clus
vv                                              22Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            23
  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                                              22Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             174
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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     4  22
  22Q GAIN WILD-TYPE  26 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4   22
  22Q GAIN WILD-TYPE   26  186
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 4                 26
  YES               22                186
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  2     4
  22Q GAIN WILD-TYPE                                6    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED                           2
  22Q GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    17
  22Q GAIN WILD-TYPE                                         1   152
D39V10, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                2                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   17                152
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     2  17
  22Q GAIN WILD-TYPE  14 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   17
  22Q GAIN WILD-TYPE   14  132
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               17                132
[1] 2 2
[1] FALSE
D39V12, continuous
D39V13, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    6  3
  22Q GAIN WILD-TYPE 65 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6    3
  22Q GAIN WILD-TYPE   65   22
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  TUMOR FREE                6                 65
  WITH TUMOR                3                 22
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  22Q GAIN MUTATED        1      0       1      1       0            20       3
  22Q GAIN WILD-TYPE     22      5       0      9       7           158      11
D39V14, multiclass
               clus
vv              22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  BRAZIL                       1                 22
  CANADA                       0                  5
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      0                  7
  UNITED STATES               20                158
  VIETNAM                      3                 11
[1] 7 2
[1] 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 11 14  0  0
  22Q GAIN WILD-TYPE 16 95 83  1 14
D39V15, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  G1                1                 16
  G2               11                 95
  G3               14                 83
  G4                0                  1
  GX                0                 14
[1] 5 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
D39V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  22Q GAIN MUTATED                                             2
  22Q GAIN WILD-TYPE                                          29
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  22Q GAIN MUTATED                5                  12
  22Q GAIN WILD-TYPE             47                 100
D39V18, multiclass
                                                 clus
vv                                                22Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 5
  LIFELONG NON-SMOKER                                           12
                                                 clus
vv                                                22Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  47
  LIFELONG NON-SMOKER                                            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"
D39V19, continuous
D39V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  22Q GAIN MUTATED             3        5             1        1
  22Q GAIN WILD-TYPE          16       70            11       11
D39V21, multiclass
               clus
vv              22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COMBINATION                  3                 16
  EXTERNAL                     5                 70
  EXTERNAL BEAM                1                 11
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V22, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  0
  22Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    0
  22Q GAIN WILD-TYPE   21    3
                         clus
vv                        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  22Q GAIN MUTATED                    0                0                   1
  22Q GAIN WILD-TYPE                  2                2                  27
                    vv
clus                 REGIONAL SITE
  22Q GAIN MUTATED               2
  22Q GAIN WILD-TYPE            14
D39V23, multiclass
                     clus
vv                    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                1                 27
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V24, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2  0
  22Q GAIN WILD-TYPE 32  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    0
  22Q GAIN WILD-TYPE   32    3
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CGY                2                 32
  GY                 0                  3
[1] 2 2
[1] FALSE
D39V25, continuous
D39V26, continuous
D39V27, continuous
D39V28, continuous
D39V29, continuous
D39V30, 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                         2                       0
  22Q GAIN WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  22Q GAIN MUTATED                         0
  22Q GAIN WILD-TYPE                       7
D39V31, multiclass
                                     clus
vv                                    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                1                  1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            2                 27
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  22Q GAIN MUTATED                                                                                   5
  22Q GAIN WILD-TYPE                                                                                63
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  22Q GAIN MUTATED                                                                                             13
  22Q GAIN WILD-TYPE                                                                                           92
D39V32, 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)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               13
                                                                                              clus
vv                                                                                             22Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            63
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V33, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    6  6
  22Q GAIN WILD-TYPE 62 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6    6
  22Q GAIN WILD-TYPE   62   64
         clus
vv        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ABSENT                 6                 62
  PRESENT                6                 64
[1] 2 2
[1] FALSE
D39V34, continuous
D39V35, continuous
D39V36, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  9
  22Q GAIN WILD-TYPE 39 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    9
  22Q GAIN WILD-TYPE   39   85
                                          clus
vv                                         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                9                 85
[1] 2 2
[1] FALSE
D39V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  22Q GAIN MUTATED              0           7          3
  22Q GAIN WILD-TYPE           10          42         54
D39V38, multiclass
              clus
vv             22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 7                 42
  NEVER USED                  3                 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"
D39V39, continuous
D39V40, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    7  0
  22Q GAIN WILD-TYPE 82 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      7    0
  22Q GAIN WILD-TYPE   82   16
         clus
vv        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ABSENT                 7                 82
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D39V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  22Q GAIN MUTATED     0    0   2    8    0  1   1    2    0   2  0   1  0   0
  22Q GAIN WILD-TYPE   1    1  28   57   24  3   7    5    9  20  1   7  2   1
                    vv
clus                 TX
  22Q GAIN MUTATED    1
  22Q GAIN WILD-TYPE 13
D39V42, multiclass
      clus
vv     22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 2                 28
  T1B1                8                 57
  T1B2                0                 24
  T2                  1                  3
  T2A                 1                  7
  T2A1                2                  5
  T2A2                0                  9
  T2B                 2                 20
  T3                  0                  1
  T3B                 1                  7
  T4                  0                  2
  TIS                 0                  1
  TX                  1                 13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  22Q GAIN MUTATED         0        0         0         0        4         8
  22Q GAIN WILD-TYPE       4        2         1         1       27        61
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  22Q GAIN MUTATED           1        0         0          1          0
  22Q GAIN WILD-TYPE        31        3         6          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  22Q GAIN MUTATED           6         0          6         0         0
  22Q GAIN WILD-TYPE        21         1         28         3         7
D39V44, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 27
  STAGE IB1                 8                 61
  STAGE IB2                 1                 31
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 6                 21
  STAGE III                 0                  1
  STAGE IIIB                6                 28
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    28   5
  XQ GAIN WILD-TYPE 155  45
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               33               200 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5                45 
$`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-C5-A8XI TCGA-C5-A8YQ TCGA-DS-A3LQ 
       73.45        83.05       154.32         8.35        23.51        22.98 
TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PM 
       13.05        13.91        14.96        45.96         1.51         0.59 
TCGA-EK-A2RB TCGA-FU-A3NI TCGA-IR-A3LB TCGA-IR-A3LL TCGA-JX-A3Q0 TCGA-LP-A5U2 
        0.07         1.45        66.81        36.36       195.85         0.30 
TCGA-LP-A5U3 TCGA-Q1-A5R3 TCGA-Q1-A73Q TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8QA 
        0.82        15.95         5.88        10.03        14.07        23.28 
TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A954 
       49.55        16.64        42.58 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY 
        2.43        20.91        40.93        44.22        73.18        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        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19        85.55        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61         2.73        50.99        45.83        75.78        99.91 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52         6.12        20.91         4.47         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        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        17.52 
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-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-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-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       15.02        14.99        13.58        13.48         0.36        12.59 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       26.27         6.64         0.43         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
       16.08         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        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.73         1.22        23.84         0.92         2.17         0.66 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-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        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        5.13         6.71        21.11        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       29.72         0.07         4.34         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       13.35         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        10.39        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ 
       12.16        61.28        34.52        29.03        20.22        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       53.52        32.15        46.03        11.51        39.78        31.27 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
        4.73        23.24        44.88        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           195.85            182.93 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            22.98             15.53 
[1] "0.1 - 195.8 (23.0)" "0.0 - 182.9 (15.5)"
[1] "hr=" "2"  
D40V2, continuous
                   vv
clus                 T1  T2 T3+T4
  XQ GAIN MUTATED    16   3     5
  XQ GAIN WILD-TYPE 105  47     6
D40V3, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                 16               105
  T2                  3                47
  T3+T4               5                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   12  7
  XQ GAIN WILD-TYPE 99 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12    7
  XQ GAIN WILD-TYPE   99   40
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              12                99
  1               7                40
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  XQ GAIN MUTATED   11  1 15
  XQ GAIN WILD-TYPE 80  7 78
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              11                80
  M1               1                 7
  MX              15                78
[1] 3 2
[1] 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                               30
  XQ GAIN WILD-TYPE             5                              167
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  XQ GAIN MUTATED                                               1
  XQ GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  XQ GAIN MUTATED                                     2
  XQ GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  XQ GAIN MUTATED                                           0
  XQ GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  XQ GAIN MUTATED                                              0
  XQ GAIN WILD-TYPE                                            6
D40V6, multiclass
                                               clus
vv                                              XQ GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           30
  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                                              XQ GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            167
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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     4  29
  XQ GAIN WILD-TYPE  26 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4   29
  XQ GAIN WILD-TYPE   26  179
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                4                26
  YES              29               179
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     3
  XQ GAIN WILD-TYPE                                8    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED                           7
  XQ GAIN WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           0    20
  XQ GAIN WILD-TYPE                                         1   149
D40V10, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   3                15
  BLACK OR AFRICAN AMERICAN                               7                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  20               149
[1] 5 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     0  21
  XQ GAIN WILD-TYPE  16 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   21
  XQ GAIN WILD-TYPE   16  128
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              21               128
[1] 2 2
[1] FALSE
D40V12, continuous
D40V13, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   13  2
  XQ GAIN WILD-TYPE 58 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     13    2
  XQ GAIN WILD-TYPE   58   23
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  TUMOR FREE              13                58
  WITH TUMOR               2                23
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  XQ GAIN MUTATED        6      0       0      0       1            23       3
  XQ GAIN WILD-TYPE     17      5       1     10       6           155      11
D40V14, multiclass
               clus
vv              XQ GAIN MUTATED XQ GAIN WILD-TYPE
  BRAZIL                      6                17
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     1                 6
  UNITED STATES              23               155
  VIETNAM                     3                11
[1] 7 2
[1] 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 16 12  0  4
  XQ GAIN WILD-TYPE 16 90 85  1 10
D40V15, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  G1               1                16
  G2              16                90
  G3              12                85
  G4               0                 1
  GX               4                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"
D40V16, continuous
D40V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  XQ GAIN MUTATED                                             4
  XQ GAIN WILD-TYPE                                          27
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  XQ GAIN MUTATED                9                  15
  XQ GAIN WILD-TYPE             43                  97
D40V18, multiclass
                                                 clus
vv                                                XQ 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                                                9
  LIFELONG NON-SMOKER                                          15
                                                 clus
vv                                                XQ GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 43
  LIFELONG NON-SMOKER                                            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"
D40V19, continuous
D40V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  XQ GAIN MUTATED             3       13             2        1
  XQ GAIN WILD-TYPE          16       62            10       11
D40V21, multiclass
               clus
vv              XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COMBINATION                 3                16
  EXTERNAL                   13                62
  EXTERNAL BEAM               2                10
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V22, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    3  1
  XQ GAIN WILD-TYPE 22  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    1
  XQ GAIN WILD-TYPE   22    2
                         clus
vv                        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COMPLETED AS PLANNED                  3                22
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  XQ GAIN MUTATED                    0                0                   2
  XQ GAIN WILD-TYPE                  2                2                  26
                   vv
clus                REGIONAL SITE
  XQ GAIN MUTATED               3
  XQ GAIN WILD-TYPE            13
D40V23, multiclass
                     clus
vv                    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               2                26
  REGIONAL SITE                     3                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V24, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    5  0
  XQ GAIN WILD-TYPE 29  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5    0
  XQ GAIN WILD-TYPE   29    3
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CGY               5                29
  GY                0                 3
[1] 2 2
[1] FALSE
D40V25, continuous
D40V26, continuous
D40V27, continuous
D40V28, continuous
D40V29, continuous
D40V30, 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                       8
  XQ GAIN WILD-TYPE                                   6                      21
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  XQ GAIN MUTATED                         0                       2
  XQ GAIN WILD-TYPE                       1                       5
D40V31, multiclass
                                     clus
vv                                    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           8                21
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 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)
  XQ GAIN MUTATED                                               1
  XQ GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  XQ GAIN MUTATED                                                2
  XQ GAIN WILD-TYPE                                             14
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  XQ GAIN MUTATED                                                                                  11
  XQ GAIN WILD-TYPE                                                                                57
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  XQ GAIN MUTATED                                                                                             16
  XQ GAIN WILD-TYPE                                                                                           89
D40V32, multiclass
                                                                                              clus
vv                                                                                             XQ 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)                         11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              16
                                                                                              clus
vv                                                                                             XQ GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V33, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    7 10
  XQ GAIN WILD-TYPE 61 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7   10
  XQ GAIN WILD-TYPE   61   60
         clus
vv        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ABSENT                7                61
  PRESENT              10                60
[1] 2 2
[1] FALSE
D40V34, continuous
D40V35, continuous
D40V36, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    9 10
  XQ GAIN WILD-TYPE 34 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      9   10
  XQ GAIN WILD-TYPE   34   84
                                          clus
vv                                         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   9                34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              10                84
[1] 2 2
[1] FALSE
D40V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  XQ GAIN MUTATED              0           7         10
  XQ GAIN WILD-TYPE           10          42         47
D40V38, multiclass
              clus
vv             XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CURRENT USER               0                10
  FORMER USER                7                42
  NEVER USED                10                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"
D40V39, continuous
D40V40, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   13  0
  XQ GAIN WILD-TYPE 76 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     13    0
  XQ GAIN WILD-TYPE   76   16
         clus
vv        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ABSENT               13                76
  PRESENT               0                16
[1] 2 2
[1] FALSE
D40V41, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  XQ GAIN MUTATED     1    0   4    7    4  1   1    0    0   1  1   4  0   0
  XQ GAIN WILD-TYPE   0    1  26   58   20  3   7    7    9  21  0   4  2   1
                   vv
clus                TX
  XQ GAIN MUTATED    3
  XQ GAIN WILD-TYPE 11
D40V42, multiclass
      clus
vv     XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1A                1                 0
  T1A1               0                 1
  T1B                4                26
  T1B1               7                58
  T1B2               4                20
  T2                 1                 3
  T2A                1                 7
  T2A1               0                 7
  T2A2               0                 9
  T2B                1                21
  T3                 1                 0
  T3B                4                 4
  T4                 0                 2
  TIS                0                 1
  TX                 3                11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  XQ GAIN MUTATED         1        1         0         0        4         8
  XQ GAIN WILD-TYPE       3        1         1         1       27        61
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  XQ GAIN MUTATED           4        0         0          0          0
  XQ GAIN WILD-TYPE        28        3         6          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  XQ GAIN MUTATED           6         1          5         0         1
  XQ GAIN WILD-TYPE        21         0         29         3         6
D40V44, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                27
  STAGE IB1                8                61
  STAGE IB2                4                28
  STAGE II                 0                 3
  STAGE IIA                0                 6
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                6                21
  STAGE III                1                 0
  STAGE IIIB               5                29
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     6   3
  1P LOSS WILD-TYPE 177  47
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9               224 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                47 
$`1P LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A7CH TCGA-C5-A7UH TCGA-DS-A0VN TCGA-MY-A913 
       35.61        73.18       154.32        60.69       118.65         5.49 
TCGA-VS-A8EB TCGA-VS-A8Q9 TCGA-VS-A8QH 
       10.03        46.03        39.78 

$`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-A1ML 
       57.73        53.16        38.99         0.46         2.43        20.91 
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-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        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19        85.55        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       58.88        50.76        44.94        40.04        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 
       17.52         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        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       13.58        13.48         0.36        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64         1.51         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        6.71        21.11       195.85        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        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 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC 
        3.88        11.67        93.99        12.16        61.28        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       29.03        20.22        14.07        19.96        53.52        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        11.51        49.55        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             5.49              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           154.32            195.85 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            46.03             15.53 
[1] "5.5 - 154.3 (46.0)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.3"
D41V2, continuous
                   vv
clus                 T1  T2 T3+T4
  1P LOSS MUTATED     3   0     1
  1P LOSS WILD-TYPE 118  50    10
D41V3, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                  3               118
  T2                  0                50
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   1
  1P LOSS WILD-TYPE 108  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    1
  1P LOSS WILD-TYPE  108   46
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               3               108
  1               1                46
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED    3  2  2
  1P LOSS WILD-TYPE 88  6 91
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               3                88
  M1               2                 6
  MX               2                91
[1] 3 2
[1] 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                                9
  1P LOSS WILD-TYPE             5                              188
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1P LOSS MUTATED                                               0
  1P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1P LOSS MUTATED                                     1
  1P LOSS WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1P LOSS MUTATED                                           0
  1P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1P LOSS MUTATED                                              1
  1P LOSS WILD-TYPE                                            5
D41V6, multiclass
                                               clus
vv                                              1P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            9
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              1P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            188
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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   8
  1P LOSS WILD-TYPE  27 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    8
  1P LOSS WILD-TYPE   27  200
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3                27
  YES               8               200
[1] 2 2
[1] FALSE
D41V8, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                71 
       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-A1ML 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        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-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-C5-A7XC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A8XH        TCGA-C5-A8XI        TCGA-C5-A8YQ        TCGA-C5-A8YT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A8ZZ        TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DR-A0ZM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GH-A9DA        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-JW-AAVH        TCGA-JX-A3Q0        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-Q1-A73Q        TCGA-Q1-A73S        TCGA-RA-A741 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PG        TCGA-VS-A8EH        TCGA-VS-A8QM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-VS-A94Y        TCGA-VS-A94Z        TCGA-WL-A834 
"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                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED                           1
  1P LOSS WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           0    10
  1P LOSS WILD-TYPE                                         1   159
D41V10, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   0                18
  BLACK OR AFRICAN AMERICAN                               1                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               159
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2   5
  1P LOSS WILD-TYPE  14 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    5
  1P LOSS WILD-TYPE   14  144
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO               5               144
[1] 2 2
[1] FALSE
D41V12, continuous
D41V13, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  1
  1P LOSS WILD-TYPE 68 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    1
  1P LOSS WILD-TYPE   68   24
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  TUMOR FREE               3                68
  WITH TUMOR               1                24
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  1P LOSS MUTATED        3      0       0      0       0             8       0
  1P LOSS WILD-TYPE     20      5       1     10       7           170      14
D41V14, multiclass
               clus
vv              1P LOSS MUTATED 1P LOSS WILD-TYPE
  BRAZIL                      3                20
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 7
  UNITED STATES               8               170
  VIETNAM                     0                14
[1] 7 2
[1] 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  7  3  0  1
  1P LOSS WILD-TYPE 17 99 94  1 13
D41V15, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  G1               0                17
  G2               7                99
  G3               3                94
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V16, continuous
D41V17, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                71 
       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-A1ML 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        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-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-C5-A7XC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A8XH        TCGA-C5-A8XI        TCGA-C5-A8YQ        TCGA-C5-A8YT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A8ZZ        TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DR-A0ZM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GH-A9DA        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-JW-AAVH        TCGA-JX-A3Q0        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-Q1-A73Q        TCGA-Q1-A73S        TCGA-RA-A741 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PG        TCGA-VS-A8EH        TCGA-VS-A8QM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-VS-A94Y        TCGA-VS-A94Z        TCGA-WL-A834 
"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                                          31
                   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                                                 1
  1P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1P LOSS MUTATED                3                   6
  1P LOSS WILD-TYPE             49                 106
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               1
  CURRENT SMOKER                                                3
  LIFELONG NON-SMOKER                                           6
                                                 clus
vv                                                1P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 49
  LIFELONG NON-SMOKER                                           106
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V19, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                65 
       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-C5-A8XI        TCGA-C5-A8YQ        TCGA-C5-A8YT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A8ZZ        TCGA-C5-A907        TCGA-DG-A2KK        TCGA-DR-A0ZM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-EA-A556        TCGA-EK-A2RA        TCGA-EX-A1H5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A770        TCGA-GH-A9DA        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-JW-AAVH        TCGA-JX-A3Q0        TCGA-MU-A5YI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-Q1-A73Q        TCGA-Q1-A73S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PG        TCGA-VS-A8EH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-VS-A8QF        TCGA-VS-A8QM        TCGA-VS-A94Y        TCGA-VS-A94Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-WL-A834 
"1P LOSS WILD-TYPE" 
D41V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  1P LOSS MUTATED             1        3             2        2
  1P LOSS WILD-TYPE          18       72            10       10
D41V21, multiclass
               clus
vv              1P LOSS MUTATED 1P LOSS WILD-TYPE
  COMBINATION                 1                18
  EXTERNAL                    3                72
  EXTERNAL BEAM               2                10
  INTERNAL                    2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V22, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  0
  1P LOSS WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    0
  1P LOSS WILD-TYPE   23    3
                         clus
vv                        1P LOSS MUTATED 1P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  1P LOSS MUTATED                    0                0                   3
  1P LOSS WILD-TYPE                  2                2                  25
                   vv
clus                REGIONAL SITE
  1P LOSS MUTATED               1
  1P LOSS WILD-TYPE            15
D41V23, multiclass
                     clus
vv                    1P LOSS MUTATED 1P LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               3                25
  REGIONAL SITE                     1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V24, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  1
  1P LOSS WILD-TYPE 32  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    1
  1P LOSS WILD-TYPE   32    2
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  CGY               2                32
  GY                1                 2
[1] 2 2
[1] FALSE
D41V25, continuous
D41V26, continuous
D41V27, continuous
D41V28, continuous
D41V29, continuous
D41V30, 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                       2
  1P LOSS WILD-TYPE                                   6                      27
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1P LOSS MUTATED                         0                       0
  1P LOSS WILD-TYPE                       1                       7
D41V31, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                43 
       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-A1M5        TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MJ        TCGA-C5-A1MP 
"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-A2M1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A3HE        TCGA-C5-A3HL        TCGA-C5-A7CJ        TCGA-C5-A7UC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7X8        TCGA-C5-A7XC        TCGA-C5-A8XH        TCGA-C5-A8XI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DG-A2KL        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        TCGA-VS-A8QA 
"1P LOSS WILD-TYPE" "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                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1P LOSS MUTATED                                                                                   3
  1P LOSS WILD-TYPE                                                                                65
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1P LOSS MUTATED                                                                                              4
  1P LOSS WILD-TYPE                                                                                          101
D41V32, multiclass
                                                                                              clus
vv                                                                                             1P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               4
                                                                                              clus
vv                                                                                             1P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V33, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  1
  1P LOSS WILD-TYPE 65 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    1
  1P LOSS WILD-TYPE   65   69
         clus
vv        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ABSENT                3                65
  PRESENT               1                69
[1] 2 2
[1] FALSE
D41V34, continuous
D41V35, continuous
D41V36, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  0
  1P LOSS WILD-TYPE 40 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE   40   94
                                          clus
vv                                         1P LOSS MUTATED 1P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   3                40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               0                94
[1] 2 2
[1] FALSE
D41V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1P LOSS MUTATED              1           2          1
  1P LOSS WILD-TYPE            9          47         56
D41V38, multiclass
              clus
vv             1P LOSS MUTATED 1P LOSS WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                2                47
  NEVER USED                 1                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"
D41V39, continuous
D41V40, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    4  0
  1P LOSS WILD-TYPE 85 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    0
  1P LOSS WILD-TYPE   85   16
         clus
vv        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ABSENT                4                85
  PRESENT               0                16
[1] 2 2
[1] FALSE
D41V41, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  1P LOSS MUTATED     0    0   1    1    1  0   0    0    0   0  0   1  0   1
  1P LOSS WILD-TYPE   1    1  29   64   23  4   8    7    9  22  1   7  2   0
                   vv
clus                TX
  1P LOSS MUTATED    2
  1P LOSS WILD-TYPE 12
D41V42, multiclass
      clus
vv     1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                1                29
  T1B1               1                64
  T1B2               1                23
  T2                 0                 4
  T2A                0                 8
  T2A1               0                 7
  T2A2               0                 9
  T2B                0                22
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                1                 0
  TX                 2                12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  1P LOSS MUTATED         0        0         0         0        2         3
  1P LOSS WILD-TYPE       4        2         1         1       29        66
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  1P LOSS MUTATED           0        0         2          0          0
  1P LOSS WILD-TYPE        32        3         4          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  1P LOSS MUTATED           1         0          3         0         0
  1P LOSS WILD-TYPE        26         1         31         3         7
D41V44, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 2                29
  STAGE IB1                3                66
  STAGE IB2                0                32
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                1                26
  STAGE III                0                 1
  STAGE IIIB               3                31
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     6   3
  1Q LOSS WILD-TYPE 177  47
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               224 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                47 
$`1Q LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A7UH TCGA-DS-A0VN 
       35.61        73.18        73.45       154.32        60.69       118.65 
TCGA-HM-A3JJ TCGA-MY-A913 TCGA-VS-A8QH 
       21.67         5.49        39.78 

$`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-A1ML 
       57.73        53.16        38.99         0.46         2.43        20.91 
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-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      182.93       101.82       134.33        15.48        20.35       147.35 
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-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       50.99        45.83         8.35        75.78        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52         6.12        20.91         4.47         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         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        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.48         0.36        12.59        45.96        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         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-A3GK 
       23.70         2.24         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        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        6.12         4.73         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-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41         7.13        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       26.56        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        10.06         5.13         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
      195.85        30.31         7.99        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        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        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       20.22        14.07        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        11.51        49.55        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             5.49              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           154.32            195.85 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            60.69             15.25 
[1] "5.5 - 154.3 (60.7)" "0.0 - 195.8 (15.2)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                 T1  T2 T3+T4
  1Q LOSS MUTATED     5   0     0
  1Q LOSS WILD-TYPE 116  50    11
D42V3, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                  5               116
  T2                  0                50
  T3+T4               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3   3
  1Q LOSS WILD-TYPE 108  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    3
  1Q LOSS WILD-TYPE  108   44
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               3               108
  1               3                44
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1Q LOSS MUTATED    3  1  3
  1Q LOSS WILD-TYPE 88  7 90
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               3                88
  M1               1                 7
  MX               3                90
[1] 3 2
[1] 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                                8
  1Q LOSS WILD-TYPE             5                              189
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1Q LOSS MUTATED                                               0
  1Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1Q LOSS MUTATED                                     0
  1Q LOSS WILD-TYPE                                  22
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1Q LOSS MUTATED                                           0
  1Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1Q LOSS MUTATED                                              1
  1Q LOSS WILD-TYPE                                            5
D42V6, multiclass
                                               clus
vv                                              1Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            8
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              1Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            189
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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   5
  1Q LOSS WILD-TYPE  26 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    5
  1Q LOSS WILD-TYPE   26  203
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                4                26
  YES               5               203
[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                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED                           3
  1Q LOSS WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0     6
  1Q LOSS WILD-TYPE                                         1   163
D42V10, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   0                18
  BLACK OR AFRICAN AMERICAN                               3                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               163
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1   7
  1Q LOSS WILD-TYPE  15 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    7
  1Q LOSS WILD-TYPE   15  142
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO               7               142
[1] 2 2
[1] FALSE
D42V12, continuous
D42V13, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    4  2
  1Q LOSS WILD-TYPE 67 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    2
  1Q LOSS WILD-TYPE   67   23
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  TUMOR FREE               4                67
  WITH TUMOR               2                23
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  1Q LOSS MUTATED        1      0       0      0       0             8       0
  1Q LOSS WILD-TYPE     22      5       1     10       7           170      14
D42V14, multiclass
               clus
vv              1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  BRAZIL                      1                22
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 7
  UNITED STATES               8               170
  VIETNAM                     0                14
[1] 7 2
[1] 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   4   5   0   0
  1Q LOSS WILD-TYPE  17 102  92   1  14
D42V15, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  G1               0                17
  G2               4               102
  G3               5                92
  G4               0                 1
  GX               0                14
[1] 5 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                                          31
                   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                                                 1
  1Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1Q LOSS MUTATED                3                   4
  1Q LOSS WILD-TYPE             49                 108
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               1
  CURRENT SMOKER                                                3
  LIFELONG NON-SMOKER                                           4
                                                 clus
vv                                                1Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 49
  LIFELONG NON-SMOKER                                           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"
D42V19, continuous
D42V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  1Q LOSS MUTATED             1        1             3        2
  1Q LOSS WILD-TYPE          18       74             9       10
D42V21, multiclass
               clus
vv              1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COMBINATION                 1                18
  EXTERNAL                    1                74
  EXTERNAL BEAM               3                 9
  INTERNAL                    2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V22, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  0
  1Q LOSS WILD-TYPE 22  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE   22    3
                         clus
vv                        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  3                22
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  1Q LOSS MUTATED                    0                1                   2
  1Q LOSS WILD-TYPE                  2                1                  26
                   vv
clus                REGIONAL SITE
  1Q LOSS MUTATED               1
  1Q LOSS WILD-TYPE            15
D42V23, multiclass
                     clus
vv                    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               2                26
  REGIONAL SITE                     1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V24, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    2  1
  1Q LOSS WILD-TYPE 32  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    1
  1Q LOSS WILD-TYPE   32    2
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CGY               2                32
  GY                1                 2
[1] 2 2
[1] FALSE
D42V25, continuous
D42V26, continuous
D42V27, continuous
D42V28, continuous
D42V29, continuous
D42V30, 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                       3
  1Q LOSS WILD-TYPE                                   6                      26
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1Q LOSS MUTATED                         0                       0
  1Q LOSS WILD-TYPE                       1                       7
D42V31, multiclass
                                     clus
vv                                    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           3                26
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1Q LOSS MUTATED                                                                                   1
  1Q LOSS WILD-TYPE                                                                                67
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1Q LOSS MUTATED                                                                                              5
  1Q LOSS WILD-TYPE                                                                                          100
D42V32, multiclass
                                                                                              clus
vv                                                                                             1Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          1
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               5
                                                                                              clus
vv                                                                                             1Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V33, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  2
  1Q LOSS WILD-TYPE 65 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE   65   68
         clus
vv        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ABSENT                3                65
  PRESENT               2                68
[1] 2 2
[1] FALSE
D42V34, continuous
D42V35, continuous
D42V36, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  2
  1Q LOSS WILD-TYPE 40 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE   40   92
                                          clus
vv                                         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   3                40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               2                92
[1] 2 2
[1] FALSE
D42V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1Q LOSS MUTATED              1           3          1
  1Q LOSS WILD-TYPE            9          46         56
D42V38, multiclass
              clus
vv             1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                3                46
  NEVER USED                 1                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"
D42V39, continuous
D42V40, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    4  0
  1Q LOSS WILD-TYPE 85 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    0
  1Q LOSS WILD-TYPE   85   16
         clus
vv        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ABSENT                4                85
  PRESENT               0                16
[1] 2 2
[1] FALSE
D42V41, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  1Q LOSS MUTATED     0    0   2    2    1  0   0    0    0   0  0   0  0   1
  1Q LOSS WILD-TYPE   1    1  28   63   23  4   8    7    9  22  1   8  2   0
                   vv
clus                TX
  1Q LOSS MUTATED    1
  1Q LOSS WILD-TYPE 13
D42V42, multiclass
      clus
vv     1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                2                28
  T1B1               2                63
  T1B2               1                23
  T2                 0                 4
  T2A                0                 8
  T2A1               0                 7
  T2A2               0                 9
  T2B                0                22
  T3                 0                 1
  T3B                0                 8
  T4                 0                 2
  TIS                1                 0
  TX                 1                13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  1Q LOSS MUTATED         0        0         0         0        3         3
  1Q LOSS WILD-TYPE       4        2         1         1       28        66
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  1Q LOSS MUTATED           0        0         1          0          0
  1Q LOSS WILD-TYPE        32        3         5          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  1Q LOSS MUTATED           1         0          1         0         0
  1Q LOSS WILD-TYPE        26         1         33         3         7
D42V44, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                28
  STAGE IB1                3                66
  STAGE IB2                0                32
  STAGE II                 0                 3
  STAGE IIA                1                 5
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                1                26
  STAGE III                0                 1
  STAGE IIIB               1                33
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    12   3
  2P LOSS WILD-TYPE 171  47
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               218 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                47 
$`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-EA-A97N TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2RN TCGA-Q1-A5R1 
       13.05         0.36         1.51         1.45         0.10        15.58 
TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A8QC 
       12.16        53.52        11.51 

$`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-A1ML TCGA-C5-A1MN 
       53.16        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43         0.82        52.01        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19        85.55        60.69        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       58.88        50.76        44.94        40.04        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 
       17.52         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-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        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
       12.59        45.96        26.27         6.64         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         0.13        16.08         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-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        6.71        21.11       195.85        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
        0.03         5.42        29.72         0.07         4.34         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
        3.88        11.67        93.99        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       29.03        20.22        14.07        19.96        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.10              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           182.93            195.85 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           13.050            16.015 
[1] "0.1 - 182.9 (13.1)" "0.0 - 195.8 (16.0)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                 T1  T2 T3+T4
  2P LOSS MUTATED     8   3     1
  2P LOSS WILD-TYPE 113  47    10
D43V3, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1                  8               113
  T2                  3                47
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7   4
  2P LOSS WILD-TYPE 104  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7    4
  2P LOSS WILD-TYPE  104   43
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               7               104
  1               4                43
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2P LOSS MUTATED    7  0  6
  2P LOSS WILD-TYPE 84  8 87
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               7                84
  M1               0                 8
  MX               6                87
[1] 3 2
[1] 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                               14
  2P LOSS WILD-TYPE             5                              183
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2P LOSS MUTATED                                               0
  2P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2P LOSS MUTATED                                     0
  2P LOSS WILD-TYPE                                  22
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2P LOSS MUTATED                                           0
  2P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2P LOSS MUTATED                                              1
  2P LOSS WILD-TYPE                                            5
D43V6, multiclass
                                               clus
vv                                              2P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           14
  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                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            183
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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  13
  2P LOSS WILD-TYPE  28 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   13
  2P LOSS WILD-TYPE   28  195
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                2                28
  YES              13               195
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                71 
       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-A1ML 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7XC        TCGA-C5-A8XH        TCGA-C5-A8XI        TCGA-C5-A8YQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A8YT        TCGA-C5-A8ZZ        TCGA-DG-A2KK        TCGA-DG-A2KL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A770        TCGA-GH-A9DA        TCGA-HM-A4S6        TCGA-HM-A6W2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JW-AAVH        TCGA-JX-A3Q0        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-Q1-A73Q        TCGA-Q1-A73S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-VS-A8EH        TCGA-VS-A8QM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-VS-A94Y        TCGA-VS-A94Z        TCGA-WL-A834 
"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                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED                           2
  2P LOSS WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    13
  2P LOSS WILD-TYPE                                         1   156
D43V10, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   0                18
  BLACK OR AFRICAN AMERICAN                               2                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               156
[1] 5 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  10
  2P LOSS WILD-TYPE  16 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE   16  139
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              10               139
[1] 2 2
[1] FALSE
D43V12, continuous
D43V13, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    4  1
  2P LOSS WILD-TYPE 67 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    1
  2P LOSS WILD-TYPE   67   24
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  TUMOR FREE               4                67
  WITH TUMOR               1                24
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  2P LOSS MUTATED        2      0       0      1       1            11       0
  2P LOSS WILD-TYPE     21      5       1      9       6           167      14
D43V14, multiclass
               clus
vv              2P LOSS MUTATED 2P LOSS WILD-TYPE
  BRAZIL                      2                21
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     1                 6
  UNITED STATES              11               167
  VIETNAM                     0                14
[1] 7 2
[1] 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    1  7  7  0  0
  2P LOSS WILD-TYPE 16 99 90  1 14
D43V15, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  G1               1                16
  G2               7                99
  G3               7                90
  G4               0                 1
  GX               0                14
[1] 5 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                33 
       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-C5-A8XH        TCGA-C5-A907 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA        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-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-VS-A8QF        TCGA-VS-A94Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-WL-A834 
"2P LOSS WILD-TYPE" 
D43V17, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                71 
       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-A1ML 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7XC        TCGA-C5-A8XH        TCGA-C5-A8XI        TCGA-C5-A8YQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A8YT        TCGA-C5-A8ZZ        TCGA-DG-A2KK        TCGA-DG-A2KL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A770        TCGA-GH-A9DA        TCGA-HM-A4S6        TCGA-HM-A6W2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JW-AAVH        TCGA-JX-A3Q0        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-Q1-A73Q        TCGA-Q1-A73S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-VS-A8EH        TCGA-VS-A8QM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-VS-A94Y        TCGA-VS-A94Z        TCGA-WL-A834 
"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                                          31
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2P LOSS MUTATED                3                   8
  2P LOSS WILD-TYPE             49                 104
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                                                3
  LIFELONG NON-SMOKER                                           8
                                                 clus
vv                                                2P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 49
  LIFELONG NON-SMOKER                                           104
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V19, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                66 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A2LS        TCGA-C5-A2LT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7X8        TCGA-C5-A8XI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A8YQ        TCGA-C5-A8YT        TCGA-C5-A8ZZ        TCGA-C5-A907 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DG-A2KK        TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-EA-A556 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EK-A2RA        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770        TCGA-GH-A9DA 
"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-JW-AAVH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Q1-A73Q        TCGA-Q1-A73S        TCGA-RA-A741        TCGA-UC-A7PD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-VS-A8EH        TCGA-VS-A8QF        TCGA-VS-A8QM        TCGA-VS-A94Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-VS-A94Z        TCGA-WL-A834 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  2P LOSS MUTATED             1        5             1        0
  2P LOSS WILD-TYPE          18       70            11       12
D43V21, multiclass
               clus
vv              2P LOSS MUTATED 2P LOSS WILD-TYPE
  COMBINATION                 1                18
  EXTERNAL                    5                70
  EXTERNAL BEAM               1                11
  INTERNAL                    0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V22, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    1  0
  2P LOSS WILD-TYPE 24  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    0
  2P LOSS WILD-TYPE   24    3
                         clus
vv                        2P LOSS MUTATED 2P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  1                24
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  2P LOSS MUTATED                    0                0                   2
  2P LOSS WILD-TYPE                  2                2                  26
                   vv
clus                REGIONAL SITE
  2P LOSS MUTATED               1
  2P LOSS WILD-TYPE            15
D43V23, multiclass
                     clus
vv                    2P LOSS MUTATED 2P LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               2                26
  REGIONAL SITE                     1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V24, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3  0
  2P LOSS WILD-TYPE 31  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    0
  2P LOSS WILD-TYPE   31    3
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  CGY               3                31
  GY                0                 3
[1] 2 2
[1] FALSE
D43V25, continuous
D43V26, continuous
D43V27, continuous
D43V28, continuous
D43V29, continuous
D43V30, 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                       3
  2P LOSS WILD-TYPE                                   6                      26
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2P LOSS MUTATED                         0                       0
  2P LOSS WILD-TYPE                       1                       7
D43V31, multiclass
                                     clus
vv                                    2P LOSS MUTATED 2P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           3                26
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  2P LOSS MUTATED                                               0
  2P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  2P LOSS MUTATED                                                1
  2P LOSS WILD-TYPE                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2P LOSS MUTATED                                                                                   5
  2P LOSS WILD-TYPE                                                                                63
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2P LOSS MUTATED                                                                                              7
  2P LOSS WILD-TYPE                                                                                           98
D43V32, multiclass
                                                                                              clus
vv                                                                                             2P 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)                          5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               7
                                                                                              clus
vv                                                                                             2P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           63
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V33, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  3
  2P LOSS WILD-TYPE 62 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    3
  2P LOSS WILD-TYPE   62   67
         clus
vv        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ABSENT                6                62
  PRESENT               3                67
[1] 2 2
[1] FALSE
D43V34, continuous
D43V35, continuous
D43V36, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  7
  2P LOSS WILD-TYPE 38 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    7
  2P LOSS WILD-TYPE   38   87
                                          clus
vv                                         2P LOSS MUTATED 2P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               7                87
[1] 2 2
[1] FALSE
D43V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2P LOSS MUTATED              1           3          3
  2P LOSS WILD-TYPE            9          46         54
D43V38, multiclass
              clus
vv             2P LOSS MUTATED 2P LOSS WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                3                46
  NEVER USED                 3                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"
D43V39, continuous
D43V40, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  0
  2P LOSS WILD-TYPE 84 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    0
  2P LOSS WILD-TYPE   84   16
         clus
vv        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ABSENT                5                84
  PRESENT               0                16
[1] 2 2
[1] FALSE
D43V41, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"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 T3 T3B T4 TIS
  2P LOSS MUTATED     0    0   1    3    4  0   1    0    0   2  0   1  0   0
  2P LOSS WILD-TYPE   1    1  29   62   20  4   7    7    9  20  1   7  2   1
                   vv
clus                TX
  2P LOSS MUTATED    1
  2P LOSS WILD-TYPE 13
D43V42, multiclass
      clus
vv     2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                1                29
  T1B1               3                62
  T1B2               4                20
  T2                 0                 4
  T2A                1                 7
  T2A1               0                 7
  T2A2               0                 9
  T2B                2                20
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                0                 1
  TX                 1                13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  2P LOSS MUTATED         0        0         0         0        3         2
  2P LOSS WILD-TYPE       4        2         1         1       28        67
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  2P LOSS MUTATED           3        1         0          0          0
  2P LOSS WILD-TYPE        29        2         6          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  2P LOSS MUTATED           1         0          3         1         0
  2P LOSS WILD-TYPE        26         1         31         2         7
D43V44, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                28
  STAGE IB1                2                67
  STAGE IB2                3                29
  STAGE II                 1                 2
  STAGE IIA                0                 6
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                1                26
  STAGE III                0                 1
  STAGE IIIB               3                31
  STAGE IVA                1                 2
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    22   5
  2Q LOSS WILD-TYPE 161  45
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27               206 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                45 
$`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-C5-A8YR TCGA-DG-A2KL TCGA-DS-A0VN TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A411 
       27.52        44.94       118.65         1.32        13.05         1.35 
TCGA-EA-A44S TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2RN TCGA-EX-A69L 
       12.66         0.36         1.51         1.45         0.10        19.79 
TCGA-HM-A3JJ TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       21.67         7.99         0.20         4.34        15.58        13.35 
TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A8QC 
       12.16        53.52        11.51 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
        0.82        52.01        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       60.69        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT 
       45.83         8.35        75.78        99.91        23.51         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM 
       20.91         4.47         1.12        58.88        50.76        40.04 
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        17.52         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-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       14.50         1.81        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        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
       12.59        45.96        26.27         6.64         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         0.13        16.08         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        6.12         4.73         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-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41         7.13        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       26.56        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        10.06         5.13         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
      195.85        30.31        11.28         0.89         0.07         0.30 
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-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        5.49         2.96        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
        3.88        11.67        93.99        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       29.03        20.22        14.07        19.96        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           182.93            195.85 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           13.350            16.015 
[1] "0.1 - 182.9 (13.3)" "0.0 - 195.8 (16.0)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                 T1  T2 T3+T4
  2Q LOSS MUTATED    15   7     1
  2Q LOSS WILD-TYPE 106  43    10
D44V3, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1                 15               106
  T2                  7                43
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   15  7
  2Q LOSS WILD-TYPE 96 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     15    7
  2Q LOSS WILD-TYPE   96   40
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              15                96
  1               7                40
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2Q LOSS MUTATED   15  0 10
  2Q LOSS WILD-TYPE 76  8 83
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              15                76
  M1               0                 8
  MX              10                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED               0                               25
  2Q LOSS WILD-TYPE             5                              172
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2Q LOSS MUTATED                                               0
  2Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2Q LOSS MUTATED                                     1
  2Q LOSS WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2Q LOSS MUTATED                                           0
  2Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2Q LOSS MUTATED                                              1
  2Q LOSS WILD-TYPE                                            5
D44V6, multiclass
                                               clus
vv                                              2Q LOSS 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                1
                                               clus
vv                                              2Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            172
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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  22
  2Q LOSS WILD-TYPE  25 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5   22
  2Q LOSS WILD-TYPE   25  186
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                5                25
  YES              22               186
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     2
  2Q LOSS WILD-TYPE                                8    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED                           3
  2Q LOSS WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    21
  2Q LOSS WILD-TYPE                                         1   148
D44V10, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               3                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  21               148
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  21
  2Q LOSS WILD-TYPE  16 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   21
  2Q LOSS WILD-TYPE   16  128
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              21               128
[1] 2 2
[1] FALSE
D44V12, continuous
D44V13, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    9  2
  2Q LOSS WILD-TYPE 62 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    2
  2Q LOSS WILD-TYPE   62   23
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  TUMOR FREE               9                62
  WITH TUMOR               2                23
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  2Q LOSS MUTATED        2      1       0      2       2            19       1
  2Q LOSS WILD-TYPE     21      4       1      8       5           159      13
D44V14, multiclass
               clus
vv              2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  BRAZIL                      2                21
  CANADA                      1                 4
  NIGERIA                     0                 1
  RUSSIA                      2                 8
  UKRAINE                     2                 5
  UNITED STATES              19               159
  VIETNAM                     1                13
[1] 7 2
[1] 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    3 11 13  0  0
  2Q LOSS WILD-TYPE 14 95 84  1 14
D44V15, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  G1               3                14
  G2              11                95
  G3              13                84
  G4               0                 1
  GX               0                14
[1] 5 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                33 
       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-C5-A8XH        TCGA-C5-A907 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA        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-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-VS-A8QF        TCGA-VS-A94Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-WL-A834 
"2Q LOSS WILD-TYPE" 
D44V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2Q LOSS MUTATED                                             0
  2Q LOSS WILD-TYPE                                          31
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2Q LOSS MUTATED                5                  17
  2Q LOSS WILD-TYPE             47                  95
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                                                5
  LIFELONG NON-SMOKER                                          17
                                                 clus
vv                                                2Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 47
  LIFELONG NON-SMOKER                                            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"
D44V19, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                65 
       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-C5-A8XI        TCGA-C5-A8YQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A8YT        TCGA-C5-A8ZZ        TCGA-C5-A907        TCGA-DG-A2KK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-EA-A556        TCGA-EK-A2RA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-GH-A9DA        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-JW-AAVH        TCGA-JX-A3Q0 
"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-Q1-A73Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-VS-A8EH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-VS-A8QF        TCGA-VS-A8QM        TCGA-VS-A94Y        TCGA-VS-A94Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-WL-A834 
"2Q LOSS WILD-TYPE" 
D44V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  2Q LOSS MUTATED             2        8             3        1
  2Q LOSS WILD-TYPE          17       67             9       11
D44V21, multiclass
               clus
vv              2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COMBINATION                 2                17
  EXTERNAL                    8                67
  EXTERNAL BEAM               3                 9
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V22, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    4  0
  2Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    0
  2Q LOSS WILD-TYPE   21    3
                         clus
vv                        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  4                21
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  2Q LOSS MUTATED                    0                1                   4
  2Q LOSS WILD-TYPE                  2                1                  24
                   vv
clus                REGIONAL SITE
  2Q LOSS MUTATED               1
  2Q LOSS WILD-TYPE            15
D44V23, multiclass
                     clus
vv                    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               4                24
  REGIONAL SITE                     1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V24, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    6  0
  2Q LOSS WILD-TYPE 28  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    0
  2Q LOSS WILD-TYPE   28    3
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CGY               6                28
  GY                0                 3
[1] 2 2
[1] FALSE
D44V25, continuous
D44V26, continuous
D44V27, continuous
D44V28, continuous
D44V29, continuous
D44V30, 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                       4
  2Q LOSS WILD-TYPE                                   6                      25
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2Q LOSS MUTATED                         0                       1
  2Q LOSS WILD-TYPE                       1                       6
D44V31, multiclass
                                     clus
vv                                    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           4                25
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  2Q LOSS MUTATED                                               1
  2Q LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  2Q LOSS MUTATED                                                1
  2Q LOSS WILD-TYPE                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2Q LOSS MUTATED                                                                                  10
  2Q LOSS WILD-TYPE                                                                                58
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2Q LOSS MUTATED                                                                                             12
  2Q LOSS WILD-TYPE                                                                                           93
D44V32, multiclass
                                                                                              clus
vv                                                                                             2Q 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)                         10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              12
                                                                                              clus
vv                                                                                             2Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           58
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V33, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   11  6
  2Q LOSS WILD-TYPE 57 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11    6
  2Q LOSS WILD-TYPE   57   64
         clus
vv        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ABSENT               11                57
  PRESENT               6                64
[1] 2 2
[1] FALSE
D44V34, continuous
D44V35, continuous
D44V36, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    7 13
  2Q LOSS WILD-TYPE 36 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7   13
  2Q LOSS WILD-TYPE   36   81
                                          clus
vv                                         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              13                81
[1] 2 2
[1] FALSE
D44V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2Q LOSS MUTATED              1           7          8
  2Q LOSS WILD-TYPE            9          42         49
D44V38, multiclass
              clus
vv             2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                7                42
  NEVER USED                 8                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"
D44V39, continuous
D44V40, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   11  0
  2Q LOSS WILD-TYPE 78 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11    0
  2Q LOSS WILD-TYPE   78   16
         clus
vv        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ABSENT               11                78
  PRESENT               0                16
[1] 2 2
[1] FALSE
D44V41, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"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 T3 T3B T4 TIS
  2Q LOSS MUTATED     0    0   4    7    4  1   2    0    2   2  0   1  0   0
  2Q LOSS WILD-TYPE   1    1  26   58   20  3   6    7    7  20  1   7  2   1
                   vv
clus                TX
  2Q LOSS MUTATED    2
  2Q LOSS WILD-TYPE 12
D44V42, multiclass
      clus
vv     2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                4                26
  T1B1               7                58
  T1B2               4                20
  T2                 1                 3
  T2A                2                 6
  T2A1               0                 7
  T2A2               2                 7
  T2B                2                20
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                0                 1
  TX                 2                12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  2Q LOSS MUTATED         0        0         0         0        4         7
  2Q LOSS WILD-TYPE       4        2         1         1       27        62
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  2Q LOSS MUTATED           3        2         1          0          1
  2Q LOSS WILD-TYPE        29        1         5          5          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  2Q LOSS MUTATED           1         0          5         1         0
  2Q LOSS WILD-TYPE        26         1         29         2         7
D44V44, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                27
  STAGE IB1                7                62
  STAGE IB2                3                29
  STAGE II                 2                 1
  STAGE IIA                1                 5
  STAGE IIA1               0                 5
  STAGE IIA2               1                 6
  STAGE IIB                1                26
  STAGE III                0                 1
  STAGE IIIB               5                29
  STAGE IVA                1                 2
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    50  17
  3P LOSS WILD-TYPE 133  33
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               166 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               17                33 
$`3P LOSS MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BL 
       49.48        23.67        11.44        18.74        36.56       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LX 
       82.85         5.46        31.40        35.61        40.93        83.05 
TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 
      154.32       147.35        85.55        94.95        13.61         2.73 
TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KM TCGA-DR-A0ZL 
       45.83        75.78        23.51        20.91        40.04        87.75 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-EA-A3HS TCGA-EA-A3QD 
       36.76       117.99       118.65        16.83         0.82        13.05 
TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A97N 
        1.18         1.35        12.66        14.99        13.58         0.36 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
        6.64         0.43         0.59         0.07         4.04         0.36 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A5XV 
       20.35        23.84         0.66         1.45         3.52         1.97 
TCGA-IR-A3L7 TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-MU-A5YI 
      147.39        24.56        21.44         6.71        21.11         0.03 
TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF 
        5.49        13.35         5.88        10.39         3.88        93.99 
TCGA-VS-A8EC TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z 
       34.52        32.15        11.51        39.78         4.73        23.24 
TCGA-VS-A9U5 
       38.96 

$`3P LOSS WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BQ TCGA-C5-A1M5 
       57.04        68.84       144.16       177.04        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       46.32        30.21        35.01        57.73        53.16        38.99 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91         3.58        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.45        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-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7XC 
       15.48        20.35        17.19        60.69         9.34        50.99 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH 
        8.35        99.91        27.52         6.12         4.47         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ 
       58.88        50.76        44.94        58.88         2.66        22.98 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B 
        1.32         0.62        14.50         1.35        14.50         1.81 
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        15.02 
TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG 
       14.96        13.48        12.59        45.96        26.27         1.51 
TCGA-EK-A2PM TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RJ 
        0.59         1.45         0.13        16.08         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        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ 
        4.73         1.22         0.92         2.17         1.02         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA 
        1.48         0.82         1.35         1.32         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41         7.13        21.67        20.78        14.93         9.44 
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-A5VH TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        36.36        27.42         3.29        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       10.06         5.13       195.85        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        13.87 
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        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
        6.25        19.59        11.67        12.16        61.28        10.03 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 
       29.03        20.22        14.07        19.96        53.52        46.03 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A954 
       23.28        49.55        31.27        16.64        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       42.08        43.82        39.35        18.05 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.03              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           173.29            195.85 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            20.35             15.53 
[1] "0.0 - 173.3 (20.4)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                T1 T2 T3+T4
  3P LOSS MUTATED   33 13     1
  3P LOSS WILD-TYPE 88 37    10
D45V3, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                 33                88
  T2                 13                37
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   21 21
  3P LOSS WILD-TYPE 90 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     21   21
  3P LOSS WILD-TYPE   90   26
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              21                90
  1              21                26
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED   25  1 27
  3P LOSS WILD-TYPE 66  7 66
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              25                66
  M1               1                 7
  MX              27                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED               1                               64
  3P LOSS WILD-TYPE             4                              133
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3P LOSS MUTATED                                               0
  3P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3P LOSS MUTATED                                     0
  3P LOSS WILD-TYPE                                  22
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3P LOSS MUTATED                                           0
  3P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3P LOSS MUTATED                                              2
  3P LOSS WILD-TYPE                                            4
D45V6, multiclass
                                               clus
vv                                              3P LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           64
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              3P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            133
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  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"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    12  55
  3P LOSS WILD-TYPE  18 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     12   55
  3P LOSS WILD-TYPE   18  153
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               12                18
  YES              55               153
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  2     3
  3P LOSS WILD-TYPE                                6    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED                           7
  3P LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0    52
  3P LOSS WILD-TYPE                                         1   117
D45V10, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 6
  ASIAN                                                   3                15
  BLACK OR AFRICAN AMERICAN                               7                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  52               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"
D45V11, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     4  44
  3P LOSS WILD-TYPE  12 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4   44
  3P LOSS WILD-TYPE   12  105
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                12
  NOT HISPANIC OR LATINO              44               105
[1] 2 2
[1] FALSE
D45V12, continuous
D45V13, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   19  7
  3P LOSS WILD-TYPE 52 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     19    7
  3P LOSS WILD-TYPE   52   18
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  TUMOR FREE              19                52
  WITH TUMOR               7                18
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  3P LOSS MUTATED        7      1       0      3       2            52       2
  3P LOSS WILD-TYPE     16      4       1      7       5           126      12
D45V14, multiclass
               clus
vv              3P LOSS MUTATED 3P LOSS WILD-TYPE
  BRAZIL                      7                16
  CANADA                      1                 4
  NIGERIA                     0                 1
  RUSSIA                      3                 7
  UKRAINE                     2                 5
  UNITED STATES              52               126
  VIETNAM                     2                12
[1] 7 2
[1] 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 32 26  0  3
  3P LOSS WILD-TYPE 14 74 71  1 11
D45V15, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  G1               3                14
  G2              32                74
  G3              26                71
  G4               0                 1
  GX               3                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"
D45V16, continuous
D45V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3P LOSS MUTATED                                             9
  3P LOSS WILD-TYPE                                          22
                   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                                                 1
  3P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3P LOSS MUTATED               24                  23
  3P LOSS WILD-TYPE             28                  89
D45V18, multiclass
                                                 clus
vv                                                3P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               24
  LIFELONG NON-SMOKER                                          23
                                                 clus
vv                                                3P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 28
  LIFELONG NON-SMOKER                                            89
[1] 5 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
D45V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  3P LOSS MUTATED             9       23             3        3
  3P LOSS WILD-TYPE          10       52             9        9
D45V21, multiclass
               clus
vv              3P LOSS MUTATED 3P LOSS WILD-TYPE
  COMBINATION                 9                10
  EXTERNAL                   23                52
  EXTERNAL BEAM               3                 9
  INTERNAL                    3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V22, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   10  1
  3P LOSS WILD-TYPE 15  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    1
  3P LOSS WILD-TYPE   15    2
                         clus
vv                        3P LOSS MUTATED 3P LOSS WILD-TYPE
  COMPLETED AS PLANNED                 10                15
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  3P LOSS MUTATED                    1                1                   9
  3P LOSS WILD-TYPE                  1                1                  19
                   vv
clus                REGIONAL SITE
  3P LOSS MUTATED               5
  3P LOSS WILD-TYPE            11
D45V23, multiclass
                     clus
vv                    3P LOSS MUTATED 3P LOSS WILD-TYPE
  DISTANT RECURRENCE                1                 1
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               9                19
  REGIONAL SITE                     5                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V24, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   10  1
  3P LOSS WILD-TYPE 24  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    1
  3P LOSS WILD-TYPE   24    2
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  CGY              10                24
  GY                1                 2
[1] 2 2
[1] FALSE
D45V25, continuous
D45V26, continuous
D45V27, continuous
D45V28, continuous
D45V29, continuous
D45V30, 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                       4
  3P LOSS WILD-TYPE                                   3                      25
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3P LOSS MUTATED                         0                       3
  3P LOSS WILD-TYPE                       1                       4
D45V31, multiclass
                                     clus
vv                                    3P LOSS MUTATED 3P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               3                 3
  OTHER LOCATION, SPECIFY                           4                25
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  3P LOSS MUTATED                                               0
  3P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  3P LOSS MUTATED                                                6
  3P LOSS WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3P LOSS MUTATED                                                                                  17
  3P LOSS WILD-TYPE                                                                                51
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3P LOSS MUTATED                                                                                             30
  3P LOSS WILD-TYPE                                                                                           75
D45V32, multiclass
                                                                                              clus
vv                                                                                             3P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              30
                                                                                              clus
vv                                                                                             3P 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)                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"
D45V33, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   11 27
  3P LOSS WILD-TYPE 57 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11   27
  3P LOSS WILD-TYPE   57   43
         clus
vv        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ABSENT               11                57
  PRESENT              27                43
[1] 2 2
[1] FALSE
D45V34, continuous
D45V35, continuous
D45V36, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   16 27
  3P LOSS WILD-TYPE 27 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     16   27
  3P LOSS WILD-TYPE   27   67
                                          clus
vv                                         3P LOSS MUTATED 3P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  16                27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              27                67
[1] 2 2
[1] FALSE
D45V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3P LOSS MUTATED              2          18         13
  3P LOSS WILD-TYPE            8          31         44
D45V38, multiclass
              clus
vv             3P LOSS MUTATED 3P LOSS WILD-TYPE
  CURRENT USER               2                 8
  FORMER USER               18                31
  NEVER USED                13                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"
D45V39, continuous
D45V40, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   21  6
  3P LOSS WILD-TYPE 68 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     21    6
  3P LOSS WILD-TYPE   68   10
         clus
vv        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ABSENT               21                68
  PRESENT               6                10
[1] 2 2
[1] FALSE
D45V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  3P LOSS MUTATED     0    1   7   21    4  2   1    1    2   7  0   1  0   1
  3P LOSS WILD-TYPE   1    0  23   44   20  2   7    6    7  15  1   7  2   0
                   vv
clus                TX
  3P LOSS MUTATED    5
  3P LOSS WILD-TYPE  9
D45V42, multiclass
      clus
vv     3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               1                 0
  T1B                7                23
  T1B1              21                44
  T1B2               4                20
  T2                 2                 2
  T2A                1                 7
  T2A1               1                 6
  T2A2               2                 7
  T2B                7                15
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                1                 0
  TX                 5                 9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  3P LOSS MUTATED         1        0         1         0       13        21
  3P LOSS WILD-TYPE       3        2         0         1       18        48
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  3P LOSS MUTATED           5        0         2          1          0
  3P LOSS WILD-TYPE        27        3         4          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  3P LOSS MUTATED          10         0          9         1         2
  3P LOSS WILD-TYPE        17         1         25         2         5
D45V44, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                13                18
  STAGE IB1               21                48
  STAGE IB2                5                27
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB               10                17
  STAGE III                0                 1
  STAGE IIIB               9                25
  STAGE IVA                1                 2
  STAGE IVB                2                 5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   3
  3Q LOSS WILD-TYPE 176  47
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               223 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                47 
$`3Q LOSS MUTATED`
TCGA-C5-A7CH TCGA-C5-A7X5 TCGA-EA-A411 TCGA-EK-A2PL TCGA-EK-A2RJ TCGA-JX-A3PZ 
      154.32        13.61         1.35         0.43         1.18        21.11 
TCGA-MU-A5YI TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-VS-A8QH 
        0.03         5.88        10.39        39.78 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43         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        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        4.47         1.12        58.88        50.76        44.94        40.04 
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        17.52         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-A439 TCGA-EA-A43B TCGA-EA-A44S 
        1.18        14.50         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        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.99        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96        26.27         6.64         1.51         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36        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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        6.71       195.85        30.31         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM 
        0.07         0.30         0.82         0.20        13.87         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       29.72         0.07         4.34         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       13.35        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       15.88         6.25        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       14.07        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       11.51        49.55        31.27        16.64         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       44.88        42.58        42.08        43.82        39.35        38.96 
TCGA-WL-A834 
       18.05 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.03              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           154.32            195.85 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            8.135            16.080 
[1] "0.0 - 154.3 (8.1)"  "0.0 - 195.8 (16.1)"
[1] "hr=" "1.8"
D46V2, continuous
                   vv
clus                 T1  T2 T3+T4
  3Q LOSS MUTATED     5   0     0
  3Q LOSS WILD-TYPE 116  50    11
D46V3, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  5               116
  T2                  0                50
  T3+T4               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   1
  3Q LOSS WILD-TYPE 108  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    1
  3Q LOSS WILD-TYPE  108   46
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               3               108
  1               1                46
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3Q LOSS MUTATED    2  0  5
  3Q LOSS WILD-TYPE 89  8 88
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               2                89
  M1               0                 8
  MX               5                88
[1] 3 2
[1] 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               1                                8
  3Q LOSS WILD-TYPE             4                              189
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3Q LOSS MUTATED                                               0
  3Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3Q LOSS MUTATED                                     0
  3Q LOSS WILD-TYPE                                  22
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3Q LOSS MUTATED                                           0
  3Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3Q LOSS MUTATED                                              1
  3Q LOSS WILD-TYPE                                            5
D46V6, multiclass
                                               clus
vv                                              3Q LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                            8
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              3Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            189
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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  10
  3Q LOSS WILD-TYPE  30 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   10
  3Q LOSS WILD-TYPE   30  198
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                30
  YES              10               198
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED                           2
  3Q LOSS WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0     8
  3Q LOSS WILD-TYPE                                         1   161
D46V10, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   0                18
  BLACK OR AFRICAN AMERICAN                               2                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               161
[1] 5 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   7
  3Q LOSS WILD-TYPE  16 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    7
  3Q LOSS WILD-TYPE   16  142
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               7               142
[1] 2 2
[1] FALSE
D46V12, continuous
D46V13, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  0
  3Q LOSS WILD-TYPE 70 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    0
  3Q LOSS WILD-TYPE   70   25
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  TUMOR FREE               1                70
  WITH TUMOR               0                25
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  3Q LOSS MUTATED        1      0       0      1       0             8       0
  3Q LOSS WILD-TYPE     22      5       1      9       7           170      14
D46V14, multiclass
               clus
vv              3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  BRAZIL                      1                22
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     0                 7
  UNITED STATES               8               170
  VIETNAM                     0                14
[1] 7 2
[1] 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   6   2   0   1
  3Q LOSS WILD-TYPE  17 100  95   1  13
D46V15, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  G1               0                17
  G2               6               100
  G3               2                95
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V16, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                32 
       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-C5-A8XH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A907        TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA 
"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-JX-A3Q0        TCGA-MU-A8JM        TCGA-Q1-A6DW 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-RA-A741        TCGA-VS-A8QF        TCGA-VS-A94Z        TCGA-WL-A834 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3Q LOSS MUTATED                                             1
  3Q LOSS WILD-TYPE                                          30
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3Q LOSS MUTATED                1                   4
  3Q LOSS WILD-TYPE             51                 108
D46V18, multiclass
                                                 clus
vv                                                3Q 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                                                1
  LIFELONG NON-SMOKER                                           4
                                                 clus
vv                                                3Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 51
  LIFELONG NON-SMOKER                                           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"
D46V19, continuous
D46V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  3Q LOSS MUTATED             0        4             0        0
  3Q LOSS WILD-TYPE          19       71            12       12
D46V21, multiclass
               clus
vv              3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COMBINATION                 0                19
  EXTERNAL                    4                71
  EXTERNAL BEAM               0                12
  INTERNAL                    0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V22, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    0  0
  3Q LOSS WILD-TYPE 25  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    0
  3Q LOSS WILD-TYPE   25    3
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  3Q LOSS MUTATED                    0                0                   2
  3Q LOSS WILD-TYPE                  2                2                  26
                   vv
clus                REGIONAL SITE
  3Q LOSS MUTATED               0
  3Q LOSS WILD-TYPE            16
D46V23, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                46 
       TCGA-C5-A0TN        TCGA-C5-A1BF        TCGA-C5-A1BQ        TCGA-C5-A2LZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CM        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-A8XJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A8XK        TCGA-C5-A8YQ        TCGA-C5-A8YT        TCGA-C5-A8ZZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A907        TCGA-DG-A2KL        TCGA-DS-A7WF        TCGA-EX-A3L1 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-HM-A3JJ        TCGA-HM-A4S6        TCGA-IR-A3LF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JW-A5VG        TCGA-JX-A5QV        TCGA-MY-A913 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-R2-A69V        TCGA-UC-A7PG        TCGA-VS-A8EC        TCGA-VS-A8EG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-VS-A8EH        TCGA-VS-A8EI        TCGA-VS-A8EL        TCGA-VS-A8Q8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-VS-A8Q9        TCGA-VS-A8QC        TCGA-VS-A8QF        TCGA-VS-A94X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-VS-A94Z        TCGA-VS-A954        TCGA-VS-A957        TCGA-VS-A958 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-VS-A959        TCGA-VS-A9U5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V24, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  0
  3Q LOSS WILD-TYPE 33  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    0
  3Q LOSS WILD-TYPE   33    3
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CGY               1                33
  GY                0                 3
[1] 2 2
[1] FALSE
D46V25, continuous
D46V26, continuous
D46V27, continuous
D46V28, continuous
D46V29, continuous
D46V30, continuous
                   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                      29
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3Q LOSS MUTATED                         0                       0
  3Q LOSS WILD-TYPE                       1                       7
D46V31, 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                                             16
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3Q LOSS MUTATED                                                                                   3
  3Q LOSS WILD-TYPE                                                                                65
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3Q LOSS MUTATED                                                                                              3
  3Q LOSS WILD-TYPE                                                                                          102
D46V32, multiclass
                                                                                              clus
vv                                                                                             3Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               3
                                                                                              clus
vv                                                                                             3Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V33, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  4
  3Q LOSS WILD-TYPE 67 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    4
  3Q LOSS WILD-TYPE   67   66
         clus
vv        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ABSENT                1                67
  PRESENT               4                66
[1] 2 2
[1] FALSE
D46V34, continuous
D46V35, continuous
D46V36, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    4  5
  3Q LOSS WILD-TYPE 39 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    5
  3Q LOSS WILD-TYPE   39   89
                                          clus
vv                                         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   4                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               5                89
[1] 2 2
[1] FALSE
D46V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3Q LOSS MUTATED              0           2          1
  3Q LOSS WILD-TYPE           10          47         56
D46V38, multiclass
              clus
vv             3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CURRENT USER               0                10
  FORMER USER                2                47
  NEVER USED                 1                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"
D46V39, continuous
D46V40, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  1
  3Q LOSS WILD-TYPE 87 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    1
  3Q LOSS WILD-TYPE   87   15
         clus
vv        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ABSENT                2                87
  PRESENT               1                15
[1] 2 2
[1] FALSE
D46V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  3Q LOSS MUTATED     0    1   1    2    1  0   0    0    0   0  0   0  0   0
  3Q LOSS WILD-TYPE   1    0  29   63   23  4   8    7    9  22  1   8  2   1
                   vv
clus                TX
  3Q LOSS MUTATED    2
  3Q LOSS WILD-TYPE 12
D46V42, multiclass
      clus
vv     3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               1                 0
  T1B                1                29
  T1B1               2                63
  T1B2               1                23
  T2                 0                 4
  T2A                0                 8
  T2A1               0                 7
  T2A2               0                 9
  T2B                0                22
  T3                 0                 1
  T3B                0                 8
  T4                 0                 2
  TIS                0                 1
  TX                 2                12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  3Q LOSS MUTATED         1        0         1         0        1         3
  3Q LOSS WILD-TYPE       3        2         0         1       30        66
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  3Q LOSS MUTATED           1        0         0          0          0
  3Q LOSS WILD-TYPE        31        3         6          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  3Q LOSS MUTATED           1         0          1         0         1
  3Q LOSS WILD-TYPE        26         1         33         3         6
D46V44, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                 1                30
  STAGE IB1                3                66
  STAGE IB2                1                31
  STAGE II                 0                 3
  STAGE IIA                0                 6
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                1                26
  STAGE III                0                 1
  STAGE IIIB               1                33
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    77  25
  4P LOSS WILD-TYPE 106  25
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              102               131 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               25                25 
$`4P LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        11.44        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI 
      173.29         5.46        31.40        35.01        53.16        35.61 
TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ 
       20.91         3.58        73.18        73.45        83.05       100.14 
TCGA-C5-A3HE TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
       18.02       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK 
       60.69        94.95         9.34         2.73        45.83        99.91 
TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK 
       23.51        20.91        58.88        40.04        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
        2.66       118.65        16.83        12.36         1.32         0.82 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A78R 
       14.50         1.35        14.50         1.81        12.66        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 
        0.36        12.59        26.27         1.51         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN 
        1.45        16.08         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-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-JW-A5VK 
        1.97         9.01         7.13        21.67        78.71        20.48 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-MU-A8JM 
        7.99        11.28         0.89         0.07         0.30         5.42 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         5.49         2.96        13.35        15.95         3.39 
TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       10.39        11.67        12.16        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF 
       20.22        14.07        19.96        32.15        11.51        49.55 
TCGA-VS-A8QM TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       31.27        42.08        43.82        39.35        38.96        18.05 

$`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       154.32       101.82        85.55 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YR TCGA-C5-A8YT 
       13.61        50.99         8.35        75.78        27.52         6.12 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VM 
        4.47         1.12        50.76        44.94        58.88       117.99 
TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       22.98        16.18        17.52         8.28         0.76         1.74 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E 
        0.62        13.05         1.18         1.35        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        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RB 
       13.58        45.96         6.64         0.43         0.13         0.07 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
        4.04         0.36        23.70         0.07         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        7.92        14.70        19.79         6.12         4.73         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         9.44       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-A5VH 
       96.95        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       21.11       195.85        30.31         0.82         0.20        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        15.58        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88         5.88         6.25        19.59         3.88 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH 
       93.99        61.28        53.52        46.03        23.28        39.78 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       16.64         4.73        23.24        44.88        42.58 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           177.04            195.85 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           16.015            15.580 
[1] "0.0 - 177.0 (16.0)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                T1 T2 T3+T4
  4P LOSS MUTATED   50 21     6
  4P LOSS WILD-TYPE 71 29     5
D47V3, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                 50                71
  T2                 21                29
  T3+T4               6                 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"
D47V4, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   38 28
  4P LOSS WILD-TYPE 73 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     38   28
  4P LOSS WILD-TYPE   73   19
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              38                73
  1              28                19
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED   38  4 41
  4P LOSS WILD-TYPE 53  4 52
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              38                53
  M1               4                 4
  MX              41                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
  4P LOSS MUTATED               2                               97
  4P LOSS WILD-TYPE             3                              100
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4P LOSS MUTATED                                               2
  4P LOSS WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4P LOSS MUTATED                                     2
  4P LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4P LOSS MUTATED                                           0
  4P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4P LOSS MUTATED                                              1
  4P LOSS WILD-TYPE                                            5
D47V6, multiclass
                                               clus
vv                                              4P LOSS MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           97
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              4P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 3
  CERVICAL SQUAMOUS CELL CARCINOMA                            100
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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    16  88
  4P LOSS WILD-TYPE  14 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16   88
  4P LOSS WILD-TYPE   14  120
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               16                14
  YES              88               120
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  2     7
  4P LOSS WILD-TYPE                                6    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED                          14
  4P LOSS WILD-TYPE                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           0    74
  4P LOSS WILD-TYPE                                         1    95
D47V10, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 6
  ASIAN                                                   7                11
  BLACK OR AFRICAN AMERICAN                              14                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  74                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"
D47V11, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    3 68
  4P LOSS WILD-TYPE 13 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3   68
  4P LOSS WILD-TYPE   13   81
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              68                81
[1] 2 2
[1] FALSE
D47V12, continuous
D47V13, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   26 12
  4P LOSS WILD-TYPE 45 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     26   12
  4P LOSS WILD-TYPE   45   13
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  TUMOR FREE              26                45
  WITH TUMOR              12                13
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  4P LOSS MUTATED       14      2       1      4       4            73       6
  4P LOSS WILD-TYPE      9      3       0      6       3           105       8
D47V14, multiclass
               clus
vv              4P LOSS MUTATED 4P LOSS WILD-TYPE
  BRAZIL                     14                 9
  CANADA                      2                 3
  NIGERIA                     1                 0
  RUSSIA                      4                 6
  UKRAINE                     4                 3
  UNITED STATES              73               105
  VIETNAM                     6                 8
[1] 7 2
[1] 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    4 43 50  1  5
  4P LOSS WILD-TYPE 13 63 47  0  9
D47V15, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  G1               4                13
  G2              43                63
  G3              50                47
  G4               1                 0
  GX               5                 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"
D47V16, continuous
D47V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4P LOSS MUTATED                                            13
  4P LOSS WILD-TYPE                                          18
                   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                                                 2
  4P LOSS WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4P LOSS MUTATED               25                  42
  4P LOSS WILD-TYPE             27                  70
D47V18, multiclass
                                                 clus
vv                                                4P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               25
  LIFELONG NON-SMOKER                                          42
                                                 clus
vv                                                4P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 27
  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"
D47V19, continuous
D47V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  4P LOSS MUTATED            10       35             6        9
  4P LOSS WILD-TYPE           9       40             6        3
D47V21, multiclass
               clus
vv              4P LOSS MUTATED 4P LOSS WILD-TYPE
  COMBINATION                10                 9
  EXTERNAL                   35                40
  EXTERNAL BEAM               6                 6
  INTERNAL                    9                 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"
D47V22, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   14  1
  4P LOSS WILD-TYPE 11  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     14    1
  4P LOSS WILD-TYPE   11    2
                         clus
vv                        4P LOSS MUTATED 4P LOSS WILD-TYPE
  COMPLETED AS PLANNED                 14                11
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  4P LOSS MUTATED                    0                2                  14
  4P LOSS WILD-TYPE                  2                0                  14
                   vv
clus                REGIONAL SITE
  4P LOSS MUTATED              13
  4P LOSS WILD-TYPE             3
D47V23, multiclass
                     clus
vv                    4P LOSS MUTATED 4P LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  2                 0
  PRIMARY TUMOR FIELD              14                14
  REGIONAL SITE                    13                 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"
D47V24, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   21  2
  4P LOSS WILD-TYPE 13  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     21    2
  4P LOSS WILD-TYPE   13    1
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  CGY              21                13
  GY                2                 1
[1] 2 2
[1] FALSE
D47V25, continuous
D47V26, continuous
D47V27, continuous
D47V28, continuous
D47V29, continuous
D47V30, 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                      14
  4P LOSS WILD-TYPE                                   3                      15
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4P LOSS MUTATED                         0                       3
  4P LOSS WILD-TYPE                       1                       4
D47V31, multiclass
                                     clus
vv                                    4P LOSS MUTATED 4P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               3                 3
  OTHER LOCATION, SPECIFY                          14                15
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 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)
  4P LOSS MUTATED                                               0
  4P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4P LOSS MUTATED                                                9
  4P LOSS WILD-TYPE                                              7
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4P LOSS MUTATED                                                                                  28
  4P LOSS WILD-TYPE                                                                                40
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4P LOSS MUTATED                                                                                             46
  4P LOSS WILD-TYPE                                                                                           59
D47V32, multiclass
                                                                                              clus
vv                                                                                             4P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              46
                                                                                              clus
vv                                                                                             4P 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)                           40
  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"
D47V33, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   24 33
  4P LOSS WILD-TYPE 44 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     24   33
  4P LOSS WILD-TYPE   44   37
         clus
vv        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ABSENT               24                44
  PRESENT              33                37
[1] 2 2
[1] FALSE
D47V34, continuous
D47V35, continuous
D47V36, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   22 41
  4P LOSS WILD-TYPE 21 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     22   41
  4P LOSS WILD-TYPE   21   53
                                          clus
vv                                         4P LOSS MUTATED 4P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  22                21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              41                53
[1] 2 2
[1] FALSE
D47V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4P LOSS MUTATED              5          21         24
  4P LOSS WILD-TYPE            5          28         33
D47V38, multiclass
              clus
vv             4P LOSS MUTATED 4P LOSS WILD-TYPE
  CURRENT USER               5                 5
  FORMER USER               21                28
  NEVER USED                24                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"
D47V39, continuous
D47V40, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   32  6
  4P LOSS WILD-TYPE 57 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     32    6
  4P LOSS WILD-TYPE   57   10
         clus
vv        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ABSENT               32                57
  PRESENT               6                10
[1] 2 2
[1] FALSE
D47V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  4P LOSS MUTATED     0    0  17   23   10  2   3    4    3   9  0   6  0   1
  4P LOSS WILD-TYPE   1    1  13   42   14  2   5    3    6  13  1   2  2   0
                   vv
clus                TX
  4P LOSS MUTATED    6
  4P LOSS WILD-TYPE  8
D47V42, multiclass
      clus
vv     4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B               17                13
  T1B1              23                42
  T1B2              10                14
  T2                 2                 2
  T2A                3                 5
  T2A1               4                 3
  T2A2               3                 6
  T2B                9                13
  T3                 0                 1
  T3B                6                 2
  T4                 0                 2
  TIS                1                 0
  TX                 6                 8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  4P LOSS MUTATED         1        1         0         1       16        25
  4P LOSS WILD-TYPE       3        1         1         0       15        44
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  4P LOSS MUTATED          15        1         1          4          2
  4P LOSS WILD-TYPE        17        2         5          1          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  4P LOSS MUTATED          13         0         16         2         1
  4P LOSS WILD-TYPE        14         1         18         1         6
D47V44, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                16                15
  STAGE IB1               25                44
  STAGE IB2               15                17
  STAGE II                 1                 2
  STAGE IIA                1                 5
  STAGE IIA1               4                 1
  STAGE IIA2               2                 5
  STAGE IIB               13                14
  STAGE III                0                 1
  STAGE IIIB              16                18
  STAGE IVA                2                 1
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    54  19
  4Q LOSS WILD-TYPE 129  31
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               73               160 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               19                31 
$`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-A1ML TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HE 
       35.61        20.91        73.18        73.45        83.05        18.02 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 
       15.48        20.35       147.35        17.19        60.69         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8ZZ TCGA-DG-A2KJ 
       13.61         2.73        99.91        27.52        20.91        58.88 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 
       40.04        87.75         0.76        12.36         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
        1.81        14.89        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RJ 
       26.27         1.51         0.59         0.59         1.45         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A3NI TCGA-FU-A5XV 
        2.24         0.10        20.35         6.94         1.45         1.97 
TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-JW-A5VK TCGA-JX-A5QV TCGA-LP-A4AU TCGA-MY-A913 
        9.01        21.67        20.48         7.99        11.28         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB 
        2.96        13.35        10.39        11.67        12.16        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 
       34.52        29.03        20.22        14.07        19.96        32.15 
TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       49.55        31.27         4.73        42.08        39.35        38.96 
TCGA-WL-A834 
       18.05 

$`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       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
      134.33        85.55        94.95        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       75.78        23.51         6.12         4.47         1.12        50.76 
TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       44.94        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-A3HQ 
       22.98        16.83        16.18        17.52         8.28         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-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35        12.66        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2PL 
       15.02        14.99        14.96        13.58         6.64         0.43 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
       23.70         0.07         0.10         0.10         0.03         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         6.12         4.73         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-A770 TCGA-HG-A2PA 
        0.82         3.52         1.35         1.32         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
        7.13        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       36.36        27.42         3.29        24.56        21.44        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
        0.89         0.07         0.30         0.82         0.20        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        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI 
        5.88         6.25        19.59         3.88        93.99        61.28 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X 
       53.52        46.03        23.28        11.51        39.78        16.64 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       23.24        44.88        42.58        43.82 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           147.35            195.85 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           15.480            15.915 
[1] "0.1 - 147.3 (15.5)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.6"
D48V2, continuous
                   vv
clus                T1 T2 T3+T4
  4Q LOSS MUTATED   34 13     6
  4Q LOSS WILD-TYPE 87 37     5
D48V3, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                 34                87
  T2                 13                37
  T3+T4               6                 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"
D48V4, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   22 20
  4Q LOSS WILD-TYPE 89 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     22   20
  4Q LOSS WILD-TYPE   89   27
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              22                89
  1              20                27
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED   30  4 22
  4Q LOSS WILD-TYPE 61  4 71
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              30                61
  M1               4                 4
  MX              22                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED               1                               70
  4Q LOSS WILD-TYPE             4                              127
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4Q LOSS MUTATED                                               1
  4Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4Q LOSS MUTATED                                     2
  4Q LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4Q LOSS MUTATED                                           1
  4Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4Q LOSS MUTATED                                              1
  4Q LOSS WILD-TYPE                                            5
D48V6, multiclass
                                               clus
vv                                              4Q LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           70
  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                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            127
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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    11  65
  4Q LOSS WILD-TYPE  19 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     11   65
  4Q LOSS WILD-TYPE   19  143
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               11                19
  YES              65               143
[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                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED                          11
  4Q LOSS WILD-TYPE                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           0    54
  4Q LOSS WILD-TYPE                                         1   115
D48V10, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                              11                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  54               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"
D48V11, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     3  46
  4Q LOSS WILD-TYPE  13 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3   46
  4Q LOSS WILD-TYPE   13  103
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              46               103
[1] 2 2
[1] FALSE
D48V12, continuous
D48V13, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   18  8
  4Q LOSS WILD-TYPE 53 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     18    8
  4Q LOSS WILD-TYPE   53   17
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  TUMOR FREE              18                53
  WITH TUMOR               8                17
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  4Q LOSS MUTATED       13      2       1      4       2            51       3
  4Q LOSS WILD-TYPE     10      3       0      6       5           127      11
D48V14, multiclass
               clus
vv              4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  BRAZIL                     13                10
  CANADA                      2                 3
  NIGERIA                     1                 0
  RUSSIA                      4                 6
  UKRAINE                     2                 5
  UNITED STATES              51               127
  VIETNAM                     3                11
[1] 7 2
[1] 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    1 25 45  0  5
  4Q LOSS WILD-TYPE 16 81 52  1  9
D48V15, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  G1               1                16
  G2              25                81
  G3              45                52
  G4               0                 1
  GX               5                 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"
D48V16, continuous
D48V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4Q LOSS MUTATED                                             5
  4Q LOSS WILD-TYPE                                          26
                   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                                                 1
  4Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4Q LOSS MUTATED               20                  28
  4Q LOSS WILD-TYPE             32                  84
D48V18, multiclass
                                                 clus
vv                                                4Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               20
  LIFELONG NON-SMOKER                                          28
                                                 clus
vv                                                4Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 32
  LIFELONG NON-SMOKER                                            84
[1] 5 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
D48V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  4Q LOSS MUTATED             5       27             5        8
  4Q LOSS WILD-TYPE          14       48             7        4
D48V21, multiclass
               clus
vv              4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COMBINATION                 5                14
  EXTERNAL                   27                48
  EXTERNAL BEAM               5                 7
  INTERNAL                    8                 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"
D48V22, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9  2
  4Q LOSS WILD-TYPE 16  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9    2
  4Q LOSS WILD-TYPE   16    1
                         clus
vv                        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  4Q LOSS MUTATED                    0                2                  10
  4Q LOSS WILD-TYPE                  2                0                  18
                   vv
clus                REGIONAL SITE
  4Q LOSS MUTATED              11
  4Q LOSS WILD-TYPE             5
D48V23, multiclass
                     clus
vv                    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  2                 0
  PRIMARY TUMOR FIELD              10                18
  REGIONAL SITE                    11                 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"
D48V24, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   16  2
  4Q LOSS WILD-TYPE 18  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     16    2
  4Q LOSS WILD-TYPE   18    1
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CGY              16                18
  GY                2                 1
[1] 2 2
[1] FALSE
D48V25, continuous
D48V26, continuous
D48V27, continuous
D48V28, continuous
D48V29, continuous
D48V30, 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                       8
  4Q LOSS WILD-TYPE                                   3                      21
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4Q LOSS MUTATED                         0                       1
  4Q LOSS WILD-TYPE                       1                       6
D48V31, multiclass
                                     clus
vv                                    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               3                 3
  OTHER LOCATION, SPECIFY                           8                21
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  4Q LOSS MUTATED                                               0
  4Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4Q LOSS MUTATED                                                6
  4Q LOSS WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4Q LOSS MUTATED                                                                                  20
  4Q LOSS WILD-TYPE                                                                                48
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4Q LOSS MUTATED                                                                                             32
  4Q LOSS WILD-TYPE                                                                                           73
D48V32, multiclass
                                                                                              clus
vv                                                                                             4Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              32
                                                                                              clus
vv                                                                                             4Q 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)                           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"
D48V33, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   16 22
  4Q LOSS WILD-TYPE 52 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     16   22
  4Q LOSS WILD-TYPE   52   48
         clus
vv        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ABSENT               16                52
  PRESENT              22                48
[1] 2 2
[1] FALSE
D48V34, continuous
D48V35, continuous
D48V36, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   13 32
  4Q LOSS WILD-TYPE 30 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     13   32
  4Q LOSS WILD-TYPE   30   62
                                          clus
vv                                         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  13                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              32                62
[1] 2 2
[1] FALSE
D48V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4Q LOSS MUTATED              5          14         18
  4Q LOSS WILD-TYPE            5          35         39
D48V38, multiclass
              clus
vv             4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CURRENT USER               5                 5
  FORMER USER               14                35
  NEVER USED                18                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"
D48V39, continuous
D48V40, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   21  4
  4Q LOSS WILD-TYPE 68 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     21    4
  4Q LOSS WILD-TYPE   68   12
         clus
vv        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ABSENT               21                68
  PRESENT               4                12
[1] 2 2
[1] FALSE
D48V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  4Q LOSS MUTATED     0    0  10   18    6  2   1    2    0   8  0   6  0   1
  4Q LOSS WILD-TYPE   1    1  20   47   18  2   7    5    9  14  1   2  2   0
                   vv
clus                TX
  4Q LOSS MUTATED    3
  4Q LOSS WILD-TYPE 11
D48V42, multiclass
      clus
vv     4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B               10                20
  T1B1              18                47
  T1B2               6                18
  T2                 2                 2
  T2A                1                 7
  T2A1               2                 5
  T2A2               0                 9
  T2B                8                14
  T3                 0                 1
  T3B                6                 2
  T4                 0                 2
  TIS                1                 0
  TX                 3                11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  4Q LOSS MUTATED         0        0         0         1       10        20
  4Q LOSS WILD-TYPE       4        2         1         0       21        49
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  4Q LOSS MUTATED          11        0         2          2          0
  4Q LOSS WILD-TYPE        21        3         4          3          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  4Q LOSS MUTATED          12         0         12         0         2
  4Q LOSS WILD-TYPE        15         1         22         3         5
D48V44, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                10                21
  STAGE IB1               20                49
  STAGE IB2               11                21
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               2                 3
  STAGE IIA2               0                 7
  STAGE IIB               12                15
  STAGE III                0                 1
  STAGE IIIB              12                22
  STAGE IVA                0                 3
  STAGE IVB                2                 5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     8   8
  5P LOSS WILD-TYPE 175  42
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               16               217 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8                42 
$`5P LOSS MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A7CH 
       11.44        68.84        35.01        38.99        35.61       154.32 
TCGA-C5-A7UC TCGA-DS-A0VK TCGA-EA-A556 TCGA-EA-A97N TCGA-EK-A2RM TCGA-FU-A3HY 
       17.19        36.76        14.89         0.36         2.24         0.66 
TCGA-LP-A4AW TCGA-MY-A913 TCGA-VS-A8EH TCGA-VS-A8QH 
        0.89         5.49        20.22        39.78 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        2.43        20.91        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-A7UE TCGA-C5-A7UH 
      134.33        15.48        20.35       147.35        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       94.95         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35        75.78        99.91        23.51        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91         4.47         1.12        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       40.04        87.75        58.88         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        17.52         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-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.66        12.82         0.26         1.48        13.91        15.02 
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-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         6.64         1.51         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         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-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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         1.22        23.84         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-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41         7.13        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX 
       21.11       195.85        30.31         7.99        11.28         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        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        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       14.07        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       11.51        49.55        31.27        16.64         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       44.88        42.58        42.08        43.82        39.35        38.96 
TCGA-WL-A834 
       18.05 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.36              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           154.32            195.85 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           18.705            15.580 
[1] "0.4 - 154.3 (18.7)" "0.0 - 195.8 (15.6)"
[1] "hr=" "2.4"
D49V2, continuous
                   vv
clus                 T1  T2 T3+T4
  5P LOSS MUTATED    10   0     2
  5P LOSS WILD-TYPE 111  50     9
D49V3, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                 10               111
  T2                  0                50
  T3+T4               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6   6
  5P LOSS WILD-TYPE 105  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    6
  5P LOSS WILD-TYPE  105   41
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6               105
  1               6                41
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5P LOSS MUTATED    8  1  5
  5P LOSS WILD-TYPE 83  7 88
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               8                83
  M1               1                 7
  MX               5                88
[1] 3 2
[1] 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                               14
  5P LOSS WILD-TYPE             5                              183
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5P LOSS MUTATED                                               0
  5P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5P LOSS MUTATED                                     1
  5P LOSS WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5P LOSS MUTATED                                           1
  5P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5P LOSS MUTATED                                              1
  5P LOSS WILD-TYPE                                            5
D49V6, multiclass
                                               clus
vv                                              5P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           14
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              5P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            183
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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  12
  5P LOSS WILD-TYPE  25 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5   12
  5P LOSS WILD-TYPE   25  196
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                5                25
  YES              12               196
[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                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED                           2
  5P LOSS WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0    13
  5P LOSS WILD-TYPE                                         1   156
D49V10, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               2                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               156
[1] 5 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     1  12
  5P LOSS WILD-TYPE  15 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   12
  5P LOSS WILD-TYPE   15  137
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              12               137
[1] 2 2
[1] FALSE
D49V12, continuous
D49V13, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  5
  5P LOSS WILD-TYPE 69 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    5
  5P LOSS WILD-TYPE   69   20
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  TUMOR FREE               2                69
  WITH TUMOR               5                20
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  5P LOSS MUTATED        2      0       0      1       1            12       1
  5P LOSS WILD-TYPE     21      5       1      9       6           166      13
D49V14, multiclass
               clus
vv              5P LOSS MUTATED 5P LOSS WILD-TYPE
  BRAZIL                      2                21
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     1                 6
  UNITED STATES              12               166
  VIETNAM                     1                13
[1] 7 2
[1] 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  7  9  0  0
  5P LOSS WILD-TYPE 16 99 88  1 14
D49V15, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  G1               1                16
  G2               7                99
  G3               9                88
  G4               0                 1
  GX               0                14
[1] 5 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                33 
       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-C5-A8XH        TCGA-C5-A907 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA        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-JX-A3Q0        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-Q1-A73S        TCGA-RA-A741        TCGA-VS-A8QF        TCGA-VS-A94Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-WL-A834 
"5P LOSS WILD-TYPE" 
D49V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5P LOSS MUTATED                                             1
  5P LOSS WILD-TYPE                                          30
                   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                                                 1
  5P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5P LOSS MUTATED                4                   6
  5P LOSS WILD-TYPE             48                 106
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               1
  CURRENT SMOKER                                                4
  LIFELONG NON-SMOKER                                           6
                                                 clus
vv                                                5P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 48
  LIFELONG NON-SMOKER                                           106
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V19, continuous
D49V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  5P LOSS MUTATED             3        2             3        1
  5P LOSS WILD-TYPE          16       73             9       11
D49V21, multiclass
               clus
vv              5P LOSS MUTATED 5P LOSS WILD-TYPE
  COMBINATION                 3                16
  EXTERNAL                    2                73
  EXTERNAL BEAM               3                 9
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V22, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    4  1
  5P LOSS WILD-TYPE 21  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    1
  5P LOSS WILD-TYPE   21    2
                         clus
vv                        5P LOSS MUTATED 5P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  4                21
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  5P LOSS MUTATED                    0                1                   2
  5P LOSS WILD-TYPE                  2                1                  26
                   vv
clus                REGIONAL SITE
  5P LOSS MUTATED               1
  5P LOSS WILD-TYPE            15
D49V23, multiclass
                     clus
vv                    5P LOSS MUTATED 5P LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               2                26
  REGIONAL SITE                     1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V24, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    3  1
  5P LOSS WILD-TYPE 31  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    1
  5P LOSS WILD-TYPE   31    2
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  CGY               3                31
  GY                1                 2
[1] 2 2
[1] FALSE
D49V25, continuous
D49V26, continuous
D49V27, continuous
D49V28, continuous
D49V29, continuous
D49V30, 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                       3
  5P LOSS WILD-TYPE                                   5                      26
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5P LOSS MUTATED                         0                       1
  5P LOSS WILD-TYPE                       1                       6
D49V31, multiclass
                                     clus
vv                                    5P LOSS MUTATED 5P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           3                26
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  5P LOSS MUTATED                                               0
  5P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5P LOSS MUTATED                                                3
  5P LOSS WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5P LOSS MUTATED                                                                                   4
  5P LOSS WILD-TYPE                                                                                64
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5P LOSS MUTATED                                                                                              7
  5P LOSS WILD-TYPE                                                                                           98
D49V32, multiclass
                                                                                              clus
vv                                                                                             5P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               7
                                                                                              clus
vv                                                                                             5P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V33, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  7
  5P LOSS WILD-TYPE 66 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    7
  5P LOSS WILD-TYPE   66   63
         clus
vv        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ABSENT                2                66
  PRESENT               7                63
[1] 2 2
[1] FALSE
D49V34, continuous
D49V35, continuous
D49V36, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    5  5
  5P LOSS WILD-TYPE 38 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    5
  5P LOSS WILD-TYPE   38   89
                                          clus
vv                                         5P LOSS MUTATED 5P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               5                89
[1] 2 2
[1] FALSE
D49V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5P LOSS MUTATED              0           2          4
  5P LOSS WILD-TYPE           10          47         53
D49V38, multiclass
              clus
vv             5P LOSS MUTATED 5P LOSS WILD-TYPE
  CURRENT USER               0                10
  FORMER USER                2                47
  NEVER USED                 4                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"
D49V39, continuous
D49V40, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  1
  5P LOSS WILD-TYPE 83 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    1
  5P LOSS WILD-TYPE   83   15
         clus
vv        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ABSENT                6                83
  PRESENT               1                15
[1] 2 2
[1] FALSE
D49V41, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                11 
       TCGA-C5-A1BN        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  5P LOSS MUTATED     0    0   4    4    2  0   0    0    0   0  0   2  0   1
  5P LOSS WILD-TYPE   1    1  26   61   22  4   8    7    9  22  1   6  2   0
                   vv
clus                TX
  5P LOSS MUTATED    1
  5P LOSS WILD-TYPE 13
D49V42, multiclass
      clus
vv     5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                4                26
  T1B1               4                61
  T1B2               2                22
  T2                 0                 4
  T2A                0                 8
  T2A1               0                 7
  T2A2               0                 9
  T2B                0                22
  T3                 0                 1
  T3B                2                 6
  T4                 0                 2
  TIS                1                 0
  TX                 1                13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  5P LOSS MUTATED         0        1         0         1        3         4
  5P LOSS WILD-TYPE       4        1         1         0       28        65
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  5P LOSS MUTATED           4        0         1          0          0
  5P LOSS WILD-TYPE        28        3         5          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  5P LOSS MUTATED           1         0          2         0         0
  5P LOSS WILD-TYPE        26         1         32         3         7
D49V44, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                 3                28
  STAGE IB1                4                65
  STAGE IB2                4                28
  STAGE II                 0                 3
  STAGE IIA                1                 5
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                1                26
  STAGE III                0                 1
  STAGE IIIB               2                32
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    31  13
  5Q LOSS WILD-TYPE 152  37
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               44               189 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13                37 
$`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-C5-A8XH 
       35.61        18.02       154.32        17.19        85.55        45.83 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QT TCGA-EA-A3HR 
       87.75        36.76         2.66       117.99        12.36         1.32 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2IP 
        1.35        14.50        14.89        14.96         0.36         6.64 
TCGA-EK-A2PL TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GK TCGA-FU-A23L TCGA-FU-A2QG 
        0.43         1.18         2.24         0.10        23.84         0.92 
TCGA-FU-A3HY TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-JW-A5VI TCGA-LP-A4AW 
        0.66         1.97        25.41        21.67        24.56         0.89 
TCGA-MY-A913 TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y 
        5.49        20.22        19.96        49.55        39.78         4.73 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

$`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-A1ML 
       30.21        57.73        53.16         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF 
       78.35       100.14        38.43         0.82        52.01        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        20.35 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
      147.35        60.69        94.95         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99         8.35        75.78        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        6.12        20.91         4.47         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       44.94        40.04        58.88       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS 
       16.18        17.52         8.28         0.76         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B 
        0.62        13.05         1.18        14.50         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        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       14.99        13.58        13.48        12.59        45.96        26.27 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        1.51         0.59         0.59         1.45         0.13        16.08 
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-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.07         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A3EO 
       14.70        19.79         6.12         4.73         1.22         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-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JK 
        1.35         1.32         1.12         9.01         7.13        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       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        27.42 
TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        6.71        21.11       195.85        30.31         7.99        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        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        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       13.35        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         5.88         6.25        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       29.03        14.07        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       11.51        31.27        16.64        23.24        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       42.08        43.82        39.35 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           154.32            195.85 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           17.605            15.580 
[1] "0.1 - 154.3 (17.6)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.5"
D50V2, continuous
                   vv
clus                T1 T2 T3+T4
  5Q LOSS MUTATED   26  7     2
  5Q LOSS WILD-TYPE 95 43     9
D50V3, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                 26                95
  T2                  7                43
  T3+T4               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   20 10
  5Q LOSS WILD-TYPE 91 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     20   10
  5Q LOSS WILD-TYPE   91   37
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              20                91
  1              10                37
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED   18  2 16
  5Q LOSS WILD-TYPE 73  6 77
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              18                73
  M1               2                 6
  MX              16                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED               0                               41
  5Q LOSS WILD-TYPE             5                              156
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5Q LOSS MUTATED                                               0
  5Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5Q LOSS MUTATED                                     2
  5Q LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5Q LOSS MUTATED                                           1
  5Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5Q LOSS MUTATED                                              1
  5Q LOSS WILD-TYPE                                            5
D50V6, multiclass
                                               clus
vv                                              5Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           41
  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                                              5Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            156
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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  37
  5Q LOSS WILD-TYPE  22 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   37
  5Q LOSS WILD-TYPE   22  171
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                8                22
  YES              37               171
[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                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED                           3
  5Q LOSS WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           0    36
  5Q LOSS WILD-TYPE                                         1   133
D50V10, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                               3                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  36               133
[1] 5 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     2  29
  5Q LOSS WILD-TYPE  14 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2   29
  5Q LOSS WILD-TYPE   14  120
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              29               120
[1] 2 2
[1] FALSE
D50V12, continuous
D50V13, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    8  9
  5Q LOSS WILD-TYPE 63 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8    9
  5Q LOSS WILD-TYPE   63   16
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  TUMOR FREE               8                63
  WITH TUMOR               9                16
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  5Q LOSS MUTATED        6      0       0      4       1            31       3
  5Q LOSS WILD-TYPE     17      5       1      6       6           147      11
D50V14, multiclass
               clus
vv              5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  BRAZIL                      6                17
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      4                 6
  UKRAINE                     1                 6
  UNITED STATES              31               147
  VIETNAM                     3                11
[1] 7 2
[1] 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 17 24  0  1
  5Q LOSS WILD-TYPE 16 89 73  1 13
D50V15, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  G1               1                16
  G2              17                89
  G3              24                73
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V16, continuous
D50V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5Q LOSS MUTATED                                             6
  5Q LOSS WILD-TYPE                                          25
                   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                                                 1
  5Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5Q LOSS MUTATED               10                  18
  5Q LOSS WILD-TYPE             42                  94
D50V18, multiclass
                                                 clus
vv                                                5Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               10
  LIFELONG NON-SMOKER                                          18
                                                 clus
vv                                                5Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 42
  LIFELONG NON-SMOKER                                            94
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V19, continuous
D50V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  5Q LOSS MUTATED             5       11             4        1
  5Q LOSS WILD-TYPE          14       64             8       11
D50V21, multiclass
               clus
vv              5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COMBINATION                 5                14
  EXTERNAL                   11                64
  EXTERNAL BEAM               4                 8
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V22, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7  1
  5Q LOSS WILD-TYPE 18  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    1
  5Q LOSS WILD-TYPE   18    2
                         clus
vv                        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  7                18
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  5Q LOSS MUTATED                    0                2                   5
  5Q LOSS WILD-TYPE                  2                0                  23
                   vv
clus                REGIONAL SITE
  5Q LOSS MUTATED               2
  5Q LOSS WILD-TYPE            14
D50V23, multiclass
                     clus
vv                    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  2                 0
  PRIMARY TUMOR FIELD               5                23
  REGIONAL SITE                     2                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V24, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7  1
  5Q LOSS WILD-TYPE 27  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    1
  5Q LOSS WILD-TYPE   27    2
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CGY               7                27
  GY                1                 2
[1] 2 2
[1] FALSE
D50V25, continuous
D50V26, continuous
D50V27, continuous
D50V28, continuous
D50V29, continuous
D50V30, 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                       7
  5Q LOSS WILD-TYPE                                   5                      22
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5Q LOSS MUTATED                         0                       1
  5Q LOSS WILD-TYPE                       1                       6
D50V31, multiclass
                                     clus
vv                                    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           7                22
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  5Q LOSS MUTATED                                               0
  5Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5Q LOSS MUTATED                                                6
  5Q LOSS WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5Q LOSS MUTATED                                                                                  11
  5Q LOSS WILD-TYPE                                                                                57
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5Q LOSS MUTATED                                                                                             18
  5Q LOSS WILD-TYPE                                                                                           87
D50V32, multiclass
                                                                                              clus
vv                                                                                             5Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              18
                                                                                              clus
vv                                                                                             5Q 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)                           57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V33, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    9 17
  5Q LOSS WILD-TYPE 59 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      9   17
  5Q LOSS WILD-TYPE   59   53
         clus
vv        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ABSENT                9                59
  PRESENT              17                53
[1] 2 2
[1] FALSE
D50V34, continuous
D50V35, continuous
D50V36, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7 22
  5Q LOSS WILD-TYPE 36 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7   22
  5Q LOSS WILD-TYPE   36   72
                                          clus
vv                                         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              22                72
[1] 2 2
[1] FALSE
D50V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5Q LOSS MUTATED              2           9         10
  5Q LOSS WILD-TYPE            8          40         47
D50V38, multiclass
              clus
vv             5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CURRENT USER               2                 8
  FORMER USER                9                40
  NEVER USED                10                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"
D50V39, continuous
D50V40, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   14  4
  5Q LOSS WILD-TYPE 75 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     14    4
  5Q LOSS WILD-TYPE   75   12
         clus
vv        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ABSENT               14                75
  PRESENT               4                12
[1] 2 2
[1] FALSE
D50V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  5Q LOSS MUTATED     0    0   5   15    6  0   1    2    0   4  0   2  0   1
  5Q LOSS WILD-TYPE   1    1  25   50   18  4   7    5    9  18  1   6  2   0
                   vv
clus                TX
  5Q LOSS MUTATED    2
  5Q LOSS WILD-TYPE 12
D50V42, multiclass
      clus
vv     5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                5                25
  T1B1              15                50
  T1B2               6                18
  T2                 0                 4
  T2A                1                 7
  T2A1               2                 5
  T2A2               0                 9
  T2B                4                18
  T3                 0                 1
  T3B                2                 6
  T4                 0                 2
  TIS                1                 0
  TX                 2                12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  5Q LOSS MUTATED         0        1         0         1        7        12
  5Q LOSS WILD-TYPE       4        1         1         0       24        57
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  5Q LOSS MUTATED           8        1         1          2          0
  5Q LOSS WILD-TYPE        24        2         5          3          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  5Q LOSS MUTATED           7         0          4         0         0
  5Q LOSS WILD-TYPE        20         1         30         3         7
D50V44, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                 7                24
  STAGE IB1               12                57
  STAGE IB2                8                24
  STAGE II                 1                 2
  STAGE IIA                1                 5
  STAGE IIA1               2                 3
  STAGE IIA2               0                 7
  STAGE IIB                7                20
  STAGE III                0                 1
  STAGE IIIB               4                30
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    30   8
  6P LOSS WILD-TYPE 153  42
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               195 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                42 
$`6P LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7CO 
       49.48        19.86        30.21        73.18       182.93       147.35 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH 
       60.69         9.34        50.99        23.51        27.52         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VK TCGA-EA-A3QE TCGA-EA-A44S 
       58.88        44.94        40.04        36.76         1.18        12.66 
TCGA-EA-A556 TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RC TCGA-EK-A2RM 
       14.89        13.58        12.59         1.51         4.04         2.24 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-IR-A3L7 TCGA-JW-A5VJ 
        0.10         0.10         7.92         0.66       147.39        21.44 
TCGA-JX-A5QV TCGA-Q1-A6DT TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Y 
        7.99         3.39        53.52        11.51        49.55         4.73 
TCGA-VS-A957 TCGA-VS-A9U5 
       42.08        38.96 

$`6P 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-A1M5 
      144.16       177.04       173.29        82.85         5.46        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       31.40        46.32        35.01        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       35.61         0.46         2.43        20.91        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       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48        20.35        17.19        85.55 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95        13.61         2.73        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DR-A0ZL 
       99.91         6.12        20.91         4.47        50.76        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88         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        17.52         8.28         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
        1.32         0.82         0.62        13.05        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35        14.50         1.81        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N 
       13.91        15.02        14.99        14.96        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       45.96        26.27         6.64         0.43         0.59         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RE 
        1.45         0.13        16.08         0.07         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-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         6.12         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84         0.92         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-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85        30.31        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       29.72         0.07         4.34         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       13.35        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       20.22        14.07        19.96        32.15        46.03        23.28 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       39.78        31.27        16.64        23.24        44.88        42.58 
TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       43.82        39.35        18.05 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           182.93            195.85 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            20.65             15.58 
[1] "0.1 - 182.9 (20.6)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                 T1  T2 T3+T4
  6P LOSS MUTATED    18   8     0
  6P LOSS WILD-TYPE 103  42    11
D51V3, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                 18               103
  T2                  8                42
  T3+T4               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   13  8
  6P LOSS WILD-TYPE 98 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     13    8
  6P LOSS WILD-TYPE   98   39
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              13                98
  1               8                39
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED   16  0 12
  6P LOSS WILD-TYPE 75  8 81
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              16                75
  M1               0                 8
  MX              12                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED               1                               36
  6P LOSS WILD-TYPE             4                              161
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6P LOSS MUTATED                                               0
  6P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6P LOSS MUTATED                                     1
  6P LOSS WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6P LOSS MUTATED                                           1
  6P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6P LOSS MUTATED                                              0
  6P LOSS WILD-TYPE                                            6
D51V6, multiclass
                                               clus
vv                                              6P LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           36
  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                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            161
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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  37
  6P LOSS WILD-TYPE  28 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   37
  6P LOSS WILD-TYPE   28  171
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                2                28
  YES              37               171
[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                                7    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED                           3
  6P LOSS WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           1    28
  6P LOSS WILD-TYPE                                         0   141
D51V10, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               3                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  28               141
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  21
  6P LOSS WILD-TYPE  15 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   21
  6P LOSS WILD-TYPE   15  128
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              21               128
[1] 2 2
[1] FALSE
D51V12, continuous
D51V13, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   11  3
  6P LOSS WILD-TYPE 60 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     11    3
  6P LOSS WILD-TYPE   60   22
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  TUMOR FREE              11                60
  WITH TUMOR               3                22
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  6P LOSS MUTATED        6      4       0      2       1            25       1
  6P LOSS WILD-TYPE     17      1       1      8       6           153      13
D51V14, multiclass
               clus
vv              6P LOSS MUTATED 6P LOSS WILD-TYPE
  BRAZIL                      6                17
  CANADA                      4                 1
  NIGERIA                     0                 1
  RUSSIA                      2                 8
  UKRAINE                     1                 6
  UNITED STATES              25               153
  VIETNAM                     1                13
[1] 7 2
[1] 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    2 16 18  0  3
  6P LOSS WILD-TYPE 15 90 79  1 11
D51V15, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  G1               2                15
  G2              16                90
  G3              18                79
  G4               0                 1
  GX               3                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"
D51V16, continuous
D51V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6P LOSS MUTATED                                             6
  6P LOSS WILD-TYPE                                          25
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6P LOSS MUTATED                8                  16
  6P LOSS WILD-TYPE             44                  96
D51V18, multiclass
                                                 clus
vv                                                6P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                8
  LIFELONG NON-SMOKER                                          16
                                                 clus
vv                                                6P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 44
  LIFELONG NON-SMOKER                                            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"
D51V19, continuous
D51V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  6P LOSS MUTATED             0       14             3        3
  6P LOSS WILD-TYPE          19       61             9        9
D51V21, multiclass
               clus
vv              6P LOSS MUTATED 6P LOSS WILD-TYPE
  COMBINATION                 0                19
  EXTERNAL                   14                61
  EXTERNAL BEAM               3                 9
  INTERNAL                    3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V22, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    2  0
  6P LOSS WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    0
  6P LOSS WILD-TYPE   23    3
                         clus
vv                        6P LOSS MUTATED 6P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  6P LOSS MUTATED                    0                0                   7
  6P LOSS WILD-TYPE                  2                2                  21
                   vv
clus                REGIONAL SITE
  6P LOSS MUTATED               5
  6P LOSS WILD-TYPE            11
D51V23, multiclass
                     clus
vv                    6P LOSS MUTATED 6P LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               7                21
  REGIONAL SITE                     5                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V24, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    9  0
  6P LOSS WILD-TYPE 25  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    0
  6P LOSS WILD-TYPE   25    3
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  CGY               9                25
  GY                0                 3
[1] 2 2
[1] FALSE
D51V25, continuous
D51V26, continuous
D51V27, continuous
D51V28, continuous
D51V29, continuous
D51V30, 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                       4
  6P LOSS WILD-TYPE                                   6                      25
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6P LOSS MUTATED                         0                       2
  6P LOSS WILD-TYPE                       1                       5
D51V31, multiclass
                                     clus
vv                                    6P LOSS MUTATED 6P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           4                25
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 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)
  6P LOSS MUTATED                                               1
  6P LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  6P LOSS MUTATED                                                3
  6P LOSS WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6P LOSS MUTATED                                                                                  11
  6P LOSS WILD-TYPE                                                                                57
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6P LOSS MUTATED                                                                                             13
  6P LOSS WILD-TYPE                                                                                           92
D51V32, multiclass
                                                                                              clus
vv                                                                                             6P 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)                         11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              13
                                                                                              clus
vv                                                                                             6P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V33, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    9  9
  6P LOSS WILD-TYPE 59 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    9
  6P LOSS WILD-TYPE   59   61
         clus
vv        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ABSENT                9                59
  PRESENT               9                61
[1] 2 2
[1] FALSE
D51V34, continuous
D51V35, continuous
D51V36, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    8 11
  6P LOSS WILD-TYPE 35 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8   11
  6P LOSS WILD-TYPE   35   83
                                          clus
vv                                         6P LOSS MUTATED 6P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              11                83
[1] 2 2
[1] FALSE
D51V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6P LOSS MUTATED              3           5         11
  6P LOSS WILD-TYPE            7          44         46
D51V38, multiclass
              clus
vv             6P LOSS MUTATED 6P LOSS WILD-TYPE
  CURRENT USER               3                 7
  FORMER USER                5                44
  NEVER USED                11                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"
D51V39, continuous
D51V40, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   15  1
  6P LOSS WILD-TYPE 74 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     15    1
  6P LOSS WILD-TYPE   74   15
         clus
vv        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ABSENT               15                74
  PRESENT               1                15
[1] 2 2
[1] FALSE
D51V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  6P LOSS MUTATED     0    0   7   10    1  0   1    0    1   6  0   0  0   0
  6P LOSS WILD-TYPE   1    1  23   55   23  4   7    7    8  16  1   8  2   1
                   vv
clus                TX
  6P LOSS MUTATED    3
  6P LOSS WILD-TYPE 11
D51V42, multiclass
      clus
vv     6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                7                23
  T1B1              10                55
  T1B2               1                23
  T2                 0                 4
  T2A                1                 7
  T2A1               0                 7
  T2A2               1                 8
  T2B                6                16
  T3                 0                 1
  T3B                0                 8
  T4                 0                 2
  TIS                0                 1
  TX                 3                11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  6P LOSS MUTATED         1        0         0         0        6        13
  6P LOSS WILD-TYPE       3        2         1         1       25        56
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  6P LOSS MUTATED           2        0         1          0          0
  6P LOSS WILD-TYPE        30        3         5          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  6P LOSS MUTATED           5         0          9         1         0
  6P LOSS WILD-TYPE        22         1         25         2         7
D51V44, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 6                25
  STAGE IB1               13                56
  STAGE IB2                2                30
  STAGE II                 0                 3
  STAGE IIA                1                 5
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                5                22
  STAGE III                0                 1
  STAGE IIIB               9                25
  STAGE IVA                1                 2
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    46  10
  6Q LOSS WILD-TYPE 137  40
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               56               177 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                40 
$`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       154.32       147.35        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KH 
       94.95         9.34        50.99        23.51        27.52         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A44S 
       58.88        44.94        40.04        12.36         1.18        12.66 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RB 
       14.89        14.96        13.58        12.59         1.51         0.07 
TCGA-EK-A2RC TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-FU-A23L 
        4.04         2.24         0.10         0.10         7.92        23.84 
TCGA-FU-A3HY TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-IR-A3L7 TCGA-JW-A5VJ 
        0.66         3.52         1.35         1.32       147.39        21.44 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX TCGA-MU-A5YI TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       21.11         7.99         0.07         0.03        13.35         3.39 
TCGA-VS-A8EB TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A957 
       10.03        53.52        11.51        49.55         4.73        42.08 
TCGA-VS-A959 TCGA-VS-A9U5 
       39.35        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY 
       20.91        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-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC 
       20.42       101.82       134.33        15.48        20.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       85.55        13.61         2.73        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DR-A0ZL 
       99.91         6.12        20.91         4.47        50.76        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-A3HQ 
       16.83        16.18        17.52         8.28         0.76         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
        1.32         0.82         0.62        13.05        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35        14.50         1.81        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 
       13.91        15.02        14.99        13.48         0.36        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         6.64         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.13        16.08         0.03         0.36         1.18        23.70 
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-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         6.12         4.73         1.22         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A5XV 
        1.02         1.45         1.58         1.48         0.82         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 
      195.85        30.31        11.28         0.89         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.20        13.87         5.42        29.72         0.07         4.34 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        5.49         2.96        15.58        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC 
        3.88        11.67        93.99        12.16        61.28        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       29.03        20.22        14.07        19.96        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       23.28        39.78        31.27        16.64        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A958 TCGA-WL-A834 
       42.58        43.82        18.05 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.03              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           182.93            195.85 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           18.035            15.880 
[1] "0.0 - 182.9 (18.0)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.6"
D52V2, continuous
                   vv
clus                T1 T2 T3+T4
  6Q LOSS MUTATED   29 12     1
  6Q LOSS WILD-TYPE 92 38    10
D52V3, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                 29                92
  T2                 12                38
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   21 12
  6Q LOSS WILD-TYPE 90 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   12
  6Q LOSS WILD-TYPE   90   35
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              21                90
  1              12                35
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   22  1 22
  6Q LOSS WILD-TYPE 69  7 71
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              22                69
  M1               1                 7
  MX              22                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED               1                               53
  6Q LOSS WILD-TYPE             4                              144
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6Q LOSS MUTATED                                               0
  6Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6Q LOSS MUTATED                                     4
  6Q LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6Q LOSS MUTATED                                           1
  6Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6Q LOSS MUTATED                                              0
  6Q LOSS WILD-TYPE                                            6
D52V6, multiclass
                                               clus
vv                                              6Q LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           53
  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                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            144
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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  54
  6Q LOSS WILD-TYPE  25 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5   54
  6Q LOSS WILD-TYPE   25  154
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                5                25
  YES              54               154
[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                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED                           7
  6Q LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           1    41
  6Q LOSS WILD-TYPE                                         0   128
D52V10, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   3                15
  BLACK OR AFRICAN AMERICAN                               7                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  41               128
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2  35
  6Q LOSS WILD-TYPE  14 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   35
  6Q LOSS WILD-TYPE   14  114
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              35               114
[1] 2 2
[1] FALSE
D52V12, continuous
D52V13, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   18  4
  6Q LOSS WILD-TYPE 53 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18    4
  6Q LOSS WILD-TYPE   53   21
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  TUMOR FREE              18                53
  WITH TUMOR               4                21
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  6Q LOSS MUTATED        8      4       0      3       1            40       3
  6Q LOSS WILD-TYPE     15      1       1      7       6           138      11
D52V14, multiclass
               clus
vv              6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  BRAZIL                      8                15
  CANADA                      4                 1
  NIGERIA                     0                 1
  RUSSIA                      3                 7
  UKRAINE                     1                 6
  UNITED STATES              40               138
  VIETNAM                     3                11
[1] 7 2
[1] 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    3 25 27  0  4
  6Q LOSS WILD-TYPE 14 81 70  1 10
D52V15, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  G1               3                14
  G2              25                81
  G3              27                70
  G4               0                 1
  GX               4                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"
D52V16, continuous
D52V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6Q LOSS MUTATED                                             6
  6Q LOSS WILD-TYPE                                          25
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6Q LOSS MUTATED               14                  27
  6Q LOSS WILD-TYPE             38                  85
D52V18, multiclass
                                                 clus
vv                                                6Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               14
  LIFELONG NON-SMOKER                                          27
                                                 clus
vv                                                6Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 38
  LIFELONG NON-SMOKER                                            85
[1] 5 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
D52V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  6Q LOSS MUTATED             3       17             2        3
  6Q LOSS WILD-TYPE          16       58            10        9
D52V21, multiclass
               clus
vv              6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COMBINATION                 3                16
  EXTERNAL                   17                58
  EXTERNAL BEAM               2                10
  INTERNAL                    3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V22, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5  0
  6Q LOSS WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    0
  6Q LOSS WILD-TYPE   20    3
                         clus
vv                        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  6Q LOSS MUTATED                    0                0                   7
  6Q LOSS WILD-TYPE                  2                2                  21
                   vv
clus                REGIONAL SITE
  6Q LOSS MUTATED               6
  6Q LOSS WILD-TYPE            10
D52V23, multiclass
                     clus
vv                    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  0                 2
  PRIMARY TUMOR FIELD               7                21
  REGIONAL SITE                     6                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V24, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   11  0
  6Q LOSS WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11    0
  6Q LOSS WILD-TYPE   23    3
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CGY              11                23
  GY                0                 3
[1] 2 2
[1] FALSE
D52V25, continuous
D52V26, continuous
D52V27, continuous
D52V28, continuous
D52V29, continuous
D52V30, 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                       5
  6Q LOSS WILD-TYPE                                   5                      24
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6Q LOSS MUTATED                         0                       2
  6Q LOSS WILD-TYPE                       1                       5
D52V31, multiclass
                                     clus
vv                                    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           5                24
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 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)
  6Q LOSS MUTATED                                               1
  6Q LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  6Q LOSS MUTATED                                                5
  6Q LOSS WILD-TYPE                                             11
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6Q LOSS MUTATED                                                                                  17
  6Q LOSS WILD-TYPE                                                                                51
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6Q LOSS MUTATED                                                                                             20
  6Q LOSS WILD-TYPE                                                                                           85
D52V32, multiclass
                                                                                              clus
vv                                                                                             6Q 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)                         17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              20
                                                                                              clus
vv                                                                                             6Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              11
  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)                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V33, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   15 14
  6Q LOSS WILD-TYPE 53 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15   14
  6Q LOSS WILD-TYPE   53   56
         clus
vv        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ABSENT               15                53
  PRESENT              14                56
[1] 2 2
[1] FALSE
D52V34, continuous
D52V35, continuous
D52V36, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    8 22
  6Q LOSS WILD-TYPE 35 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      8   22
  6Q LOSS WILD-TYPE   35   72
                                          clus
vv                                         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              22                72
[1] 2 2
[1] FALSE
D52V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6Q LOSS MUTATED              3          10         16
  6Q LOSS WILD-TYPE            7          39         41
D52V38, multiclass
              clus
vv             6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CURRENT USER               3                 7
  FORMER USER               10                39
  NEVER USED                16                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"
D52V39, continuous
D52V40, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   22  4
  6Q LOSS WILD-TYPE 67 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     22    4
  6Q LOSS WILD-TYPE   67   12
         clus
vv        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ABSENT               22                67
  PRESENT               4                12
[1] 2 2
[1] FALSE
D52V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  6Q LOSS MUTATED     0    1  12   14    2  1   1    2    1   7  0   1  0   0
  6Q LOSS WILD-TYPE   1    0  18   51   22  3   7    5    8  15  1   7  2   1
                   vv
clus                TX
  6Q LOSS MUTATED    4
  6Q LOSS WILD-TYPE 10
D52V42, multiclass
      clus
vv     6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               1                 0
  T1B               12                18
  T1B1              14                51
  T1B2               2                22
  T2                 1                 3
  T2A                1                 7
  T2A1               2                 5
  T2A2               1                 8
  T2B                7                15
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                0                 1
  TX                 4                10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  6Q LOSS MUTATED         1        0         1         0       10        19
  6Q LOSS WILD-TYPE       3        2         0         1       21        50
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  6Q LOSS MUTATED           3        0         2          1          0
  6Q LOSS WILD-TYPE        29        3         4          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  6Q LOSS MUTATED           7         0         11         1         1
  6Q LOSS WILD-TYPE        20         1         23         2         6
D52V44, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 0                 2
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                10                21
  STAGE IB1               19                50
  STAGE IB2                3                29
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                7                20
  STAGE III                0                 1
  STAGE IIIB              11                23
  STAGE IVA                1                 2
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    14   7
  7P LOSS WILD-TYPE 169  43
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               21               212 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7                43 
$`7P LOSS MUTATED`
TCGA-C5-A0TN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       11.44        31.40        35.01        53.16        38.99        35.61 
TCGA-C5-A2LX TCGA-C5-A7CK TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DS-A7WH TCGA-EA-A1QS 
       83.05       134.33        13.61        87.75        17.52         0.76 
TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-JX-A3Q8 
       14.50        14.96         0.36         2.24        20.35        30.31 
TCGA-LP-A7HU TCGA-RA-A741 TCGA-VS-A957 
        0.20         3.88        42.08 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-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-A7CL 
       17.85        20.42       182.93       154.32       101.82        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34         2.73        50.99        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM 
        1.12        58.88        50.76        44.94        40.04        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-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18         8.28        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-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        15.02        14.99        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
       45.96        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         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-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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
        6.71        21.11       195.85         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.07         0.30         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       29.72         0.07         4.34         5.49         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       13.35        15.95         3.39        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD 
       15.88         5.88         6.25        10.39        19.59        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       20.22        14.07        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       23.28        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 
        4.73        23.24        44.88        42.58        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.20              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           134.33            195.85 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            20.35             15.58 
[1] "0.2 - 134.3 (20.4)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.4"
D53V2, continuous
                   vv
clus                 T1  T2 T3+T4
  7P LOSS MUTATED    10   4     1
  7P LOSS WILD-TYPE 111  46    10
D53V3, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1                 10               111
  T2                  4                46
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8   5
  7P LOSS WILD-TYPE 103  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8    5
  7P LOSS WILD-TYPE  103   42
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               8               103
  1               5                42
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7P LOSS MUTATED    8  0  7
  7P LOSS WILD-TYPE 83  8 86
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               8                83
  M1               0                 8
  MX               7                86
[1] 3 2
[1] 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                               17
  7P LOSS WILD-TYPE             5                              180
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7P LOSS MUTATED                                               0
  7P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7P LOSS MUTATED                                     4
  7P LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7P LOSS MUTATED                                           0
  7P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7P LOSS MUTATED                                              0
  7P LOSS WILD-TYPE                                            6
D53V6, multiclass
                                               clus
vv                                              7P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           17
  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                                              7P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            180
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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  13
  7P LOSS WILD-TYPE  22 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8   13
  7P LOSS WILD-TYPE   22  195
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                8                22
  YES              13               195
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     5
  7P LOSS WILD-TYPE                                8    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED                           3
  7P LOSS WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0    13
  7P LOSS WILD-TYPE                                         1   156
D53V10, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   5                13
  BLACK OR AFRICAN AMERICAN                               3                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               156
[1] 5 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  18
  7P LOSS WILD-TYPE  16 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   18
  7P LOSS WILD-TYPE   16  131
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              18               131
[1] 2 2
[1] FALSE
D53V12, continuous
D53V13, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    7  6
  7P LOSS WILD-TYPE 64 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    6
  7P LOSS WILD-TYPE   64   19
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  TUMOR FREE               7                64
  WITH TUMOR               6                19
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  7P LOSS MUTATED        1      0       0      1       1            15       3
  7P LOSS WILD-TYPE     22      5       1      9       6           163      11
D53V14, multiclass
               clus
vv              7P LOSS MUTATED 7P LOSS WILD-TYPE
  BRAZIL                      1                22
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     1                 6
  UNITED STATES              15               163
  VIETNAM                     3                11
[1] 7 2
[1] 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  8 12  0  1
  7P LOSS WILD-TYPE 17 98 85  1 13
D53V15, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  G1               0                17
  G2               8                98
  G3              12                85
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V16, continuous
D53V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7P LOSS MUTATED                                             2
  7P LOSS WILD-TYPE                                          29
                   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                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7P LOSS MUTATED                3                  12
  7P LOSS WILD-TYPE             49                 100
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                                          12
                                                 clus
vv                                                7P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 49
  LIFELONG NON-SMOKER                                           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"
D53V19, continuous
D53V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  7P LOSS MUTATED             5        5             2        0
  7P LOSS WILD-TYPE          14       70            10       12
D53V21, multiclass
               clus
vv              7P LOSS MUTATED 7P LOSS WILD-TYPE
  COMBINATION                 5                14
  EXTERNAL                    5                70
  EXTERNAL BEAM               2                10
  INTERNAL                    0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V22, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    7  1
  7P LOSS WILD-TYPE 18  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    1
  7P LOSS WILD-TYPE   18    2
                         clus
vv                        7P LOSS MUTATED 7P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  7                18
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  7P LOSS MUTATED                    0                1                   2
  7P LOSS WILD-TYPE                  2                1                  26
                   vv
clus                REGIONAL SITE
  7P LOSS MUTATED               1
  7P LOSS WILD-TYPE            15
D53V23, multiclass
                     clus
vv                    7P LOSS MUTATED 7P LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               2                26
  REGIONAL SITE                     1                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V24, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    2  0
  7P LOSS WILD-TYPE 32  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    0
  7P LOSS WILD-TYPE   32    3
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  CGY               2                32
  GY                0                 3
[1] 2 2
[1] FALSE
D53V25, continuous
D53V26, continuous
D53V27, continuous
D53V28, continuous
D53V29, continuous
D53V30, 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                       2
  7P LOSS WILD-TYPE                                   4                      27
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7P LOSS MUTATED                         0                       1
  7P LOSS WILD-TYPE                       1                       6
D53V31, multiclass
                                     clus
vv                                    7P LOSS MUTATED 7P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 4
  OTHER LOCATION, SPECIFY                           2                27
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             14
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7P LOSS MUTATED                                                                                   8
  7P LOSS WILD-TYPE                                                                                60
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7P LOSS MUTATED                                                                                              8
  7P LOSS WILD-TYPE                                                                                           97
D53V32, 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)                          8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               8
                                                                                              clus
vv                                                                                             7P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V33, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    6  8
  7P LOSS WILD-TYPE 62 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    8
  7P LOSS WILD-TYPE   62   62
         clus
vv        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ABSENT                6                62
  PRESENT               8                62
[1] 2 2
[1] FALSE
D53V34, continuous
D53V35, continuous
D53V36, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    6  8
  7P LOSS WILD-TYPE 37 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    8
  7P LOSS WILD-TYPE   37   86
                                          clus
vv                                         7P LOSS MUTATED 7P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               8                86
[1] 2 2
[1] FALSE
D53V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7P LOSS MUTATED              0           7          6
  7P LOSS WILD-TYPE           10          42         51
D53V38, multiclass
              clus
vv             7P LOSS MUTATED 7P LOSS WILD-TYPE
  CURRENT USER               0                10
  FORMER USER                7                42
  NEVER USED                 6                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"
D53V39, continuous
D53V40, binary
                   cls
clus                 0  1
  7P LOSS MUTATED   12  1
  7P LOSS WILD-TYPE 77 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     12    1
  7P LOSS WILD-TYPE   77   15
         clus
vv        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ABSENT               12                77
  PRESENT               1                15
[1] 2 2
[1] FALSE
D53V41, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2                11 
       TCGA-C5-A1BN        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  7P LOSS MUTATED     0    0   1    7    2  2   0    1    0   1  0   1  0   0
  7P LOSS WILD-TYPE   1    1  29   58   22  2   8    6    9  21  1   7  2   1
                   vv
clus                TX
  7P LOSS MUTATED    0
  7P LOSS WILD-TYPE 14
D53V42, multiclass
      clus
vv     7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                1                29
  T1B1               7                58
  T1B2               2                22
  T2                 2                 2
  T2A                0                 8
  T2A1               1                 6
  T2A2               0                 9
  T2B                1                21
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                0                 1
  TX                 0                14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  7P LOSS MUTATED         0        0         0         0        2         8
  7P LOSS WILD-TYPE       4        2         1         1       29        61
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  7P LOSS MUTATED           3        1         0          1          0
  7P LOSS WILD-TYPE        29        2         6          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  7P LOSS MUTATED           3         0          1         1         1
  7P LOSS WILD-TYPE        24         1         33         2         6
D53V44, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 2                29
  STAGE IB1                8                61
  STAGE IB2                3                29
  STAGE II                 1                 2
  STAGE IIA                0                 6
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                3                24
  STAGE III                0                 1
  STAGE IIIB               1                33
  STAGE IVA                1                 2
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    22  10
  7Q LOSS WILD-TYPE 161  40
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               32               201 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10                40 
$`7Q LOSS MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI 
       11.44         5.46        31.40        35.01        38.99        35.61 
TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7X5 
       40.93        73.45        83.05       154.32        15.48        13.61 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H0 
       17.52         0.76        14.50        14.96         0.36        45.96 
TCGA-EK-A2H1 TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A2QG 
       26.27         0.36         2.24         0.10        20.35         0.92 
TCGA-FU-A40J TCGA-HM-A3JJ TCGA-JW-A5VG TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MY-A5BF 
        1.35        21.67        27.42        30.31         0.20         4.34 
TCGA-RA-A741 TCGA-VS-A957 
        3.88        42.08 

$`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-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ 
       20.91         3.58        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-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      182.93       101.82       134.33        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
       85.55        60.69        94.95         9.34         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35        75.78        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        6.12        20.91         4.47         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        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-A7WI 
      117.99       118.65        22.98        16.83        16.18         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-A43B TCGA-EA-A44S 
        1.18        14.50         1.35         1.35         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        15.02 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG 
       14.99        13.58        13.48        12.59         6.64         1.51 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
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-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.07         0.10         0.03         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       19.79         6.12         4.73         1.22        23.84         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-GH-A9DA TCGA-HG-A2PA 
        3.52         1.32         1.97         1.12         9.01        25.41 
TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
        7.13        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       10.06         5.13         6.71        21.11       195.85         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y 
       11.28         0.89         0.07         0.30         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       29.03        20.22        14.07        19.96        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       46.03        23.28        11.51        49.55        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       16.64         4.73        23.24        44.88        42.58        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.10              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           154.32            195.85 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            16.50             15.88 
[1] "0.1 - 154.3 (16.5)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.7"
D54V2, continuous
                   vv
clus                 T1  T2 T3+T4
  7Q LOSS MUTATED    12   8     1
  7Q LOSS WILD-TYPE 109  42    10
D54V3, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1                 12               109
  T2                  8                42
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    10   8
  7Q LOSS WILD-TYPE 101  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     10    8
  7Q LOSS WILD-TYPE  101   39
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              10               101
  1               8                39
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7Q LOSS MUTATED    7  0 13
  7Q LOSS WILD-TYPE 84  8 80
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               7                84
  M1               0                 8
  MX              13                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED               0                               26
  7Q LOSS WILD-TYPE             5                              171
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7Q LOSS MUTATED                                               0
  7Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7Q LOSS MUTATED                                     6
  7Q LOSS WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7Q LOSS MUTATED                                           0
  7Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7Q LOSS MUTATED                                              0
  7Q LOSS WILD-TYPE                                            6
D54V6, multiclass
                                               clus
vv                                              7Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           26
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              7Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            171
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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    11  21
  7Q LOSS WILD-TYPE  19 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11   21
  7Q LOSS WILD-TYPE   19  187
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               11                19
  YES              21               187
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  1     4
  7Q LOSS WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED                           5
  7Q LOSS WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    22
  7Q LOSS WILD-TYPE                                         1   147
D54V10, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                               5                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  22               147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  26
  7Q LOSS WILD-TYPE  15 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   26
  7Q LOSS WILD-TYPE   15  123
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              26               123
[1] 2 2
[1] FALSE
D54V12, continuous
D54V13, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED   10  8
  7Q LOSS WILD-TYPE 61 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     10    8
  7Q LOSS WILD-TYPE   61   17
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  TUMOR FREE              10                61
  WITH TUMOR               8                17
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  7Q LOSS MUTATED        1      0       0      1       1            26       3
  7Q LOSS WILD-TYPE     22      5       1      9       6           152      11
D54V14, multiclass
               clus
vv              7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  BRAZIL                      1                22
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     1                 6
  UNITED STATES              26               152
  VIETNAM                     3                11
[1] 7 2
[1] 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 11 19  0  1
  7Q LOSS WILD-TYPE 16 95 78  1 13
D54V15, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  G1               1                16
  G2              11                95
  G3              19                78
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V16, continuous
D54V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7Q LOSS MUTATED                                             2
  7Q LOSS WILD-TYPE                                          29
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7Q LOSS MUTATED                7                  15
  7Q LOSS WILD-TYPE             45                  97
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                                          15
                                                 clus
vv                                                7Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 45
  LIFELONG NON-SMOKER                                            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"
D54V19, continuous
D54V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  7Q LOSS MUTATED             6        5             4        1
  7Q LOSS WILD-TYPE          13       70             8       11
D54V21, multiclass
               clus
vv              7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COMBINATION                 6                13
  EXTERNAL                    5                70
  EXTERNAL BEAM               4                 8
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V22, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    9  2
  7Q LOSS WILD-TYPE 16  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9    2
  7Q LOSS WILD-TYPE   16    1
                         clus
vv                        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  7Q LOSS MUTATED                    0                2                   2
  7Q LOSS WILD-TYPE                  2                0                  26
                   vv
clus                REGIONAL SITE
  7Q LOSS MUTATED               2
  7Q LOSS WILD-TYPE            14
D54V23, multiclass
                     clus
vv                    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  2                 0
  PRIMARY TUMOR FIELD               2                26
  REGIONAL SITE                     2                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V24, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    4  1
  7Q LOSS WILD-TYPE 30  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    1
  7Q LOSS WILD-TYPE   30    2
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CGY               4                30
  GY                1                 2
[1] 2 2
[1] FALSE
D54V25, continuous
D54V26, continuous
D54V27, continuous
D54V28, continuous
D54V29, continuous
D54V30, 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                       2
  7Q LOSS WILD-TYPE                                   4                      27
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7Q LOSS MUTATED                         0                       1
  7Q LOSS WILD-TYPE                       1                       6
D54V31, multiclass
                                     clus
vv                                    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 4
  OTHER LOCATION, SPECIFY                           2                27
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7Q LOSS MUTATED                                                                                   8
  7Q LOSS WILD-TYPE                                                                                60
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7Q LOSS MUTATED                                                                                             16
  7Q LOSS WILD-TYPE                                                                                           89
D54V32, 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)                          8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              16
                                                                                              clus
vv                                                                                             7Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V33, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    8 13
  7Q LOSS WILD-TYPE 60 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8   13
  7Q LOSS WILD-TYPE   60   57
         clus
vv        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ABSENT                8                60
  PRESENT              13                57
[1] 2 2
[1] FALSE
D54V34, continuous
D54V35, continuous
D54V36, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    9 12
  7Q LOSS WILD-TYPE 34 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9   12
  7Q LOSS WILD-TYPE   34   82
                                          clus
vv                                         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   9                34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              12                82
[1] 2 2
[1] FALSE
D54V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7Q LOSS MUTATED              1           9          8
  7Q LOSS WILD-TYPE            9          40         49
D54V38, multiclass
              clus
vv             7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER                9                40
  NEVER USED                 8                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"
D54V39, continuous
D54V40, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED   14  1
  7Q LOSS WILD-TYPE 75 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     14    1
  7Q LOSS WILD-TYPE   75   15
         clus
vv        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ABSENT               14                75
  PRESENT               1                15
[1] 2 2
[1] FALSE
D54V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  7Q LOSS MUTATED     0    0   2    9    1  2   1    2    2   1  0   1  0   0
  7Q LOSS WILD-TYPE   1    1  28   56   23  2   7    5    7  21  1   7  2   1
                   vv
clus                TX
  7Q LOSS MUTATED    0
  7Q LOSS WILD-TYPE 14
D54V42, multiclass
      clus
vv     7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                2                28
  T1B1               9                56
  T1B2               1                23
  T2                 2                 2
  T2A                1                 7
  T2A1               2                 5
  T2A2               2                 7
  T2B                1                21
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                0                 1
  TX                 0                14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  7Q LOSS MUTATED         0        0         0         0        2        11
  7Q LOSS WILD-TYPE       4        2         1         1       29        58
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  7Q LOSS MUTATED           4        1         2          1          1
  7Q LOSS WILD-TYPE        28        2         4          4          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  7Q LOSS MUTATED           5         0          4         0         1
  7Q LOSS WILD-TYPE        22         1         30         3         6
D54V44, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 2                29
  STAGE IB1               11                58
  STAGE IB2                4                28
  STAGE II                 1                 2
  STAGE IIA                2                 4
  STAGE IIA1               1                 4
  STAGE IIA2               1                 6
  STAGE IIB                5                22
  STAGE III                0                 1
  STAGE IIIB               4                30
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    47  18
  8P LOSS WILD-TYPE 136  32
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               65               168 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               18                32 
$`8P LOSS MUTATED`
TCGA-C5-A1BE TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       68.84        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY 
        2.43        20.91        40.93        73.18        73.45        78.35 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK 
       94.95        13.61         2.73        50.99        45.83        99.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WI 
        4.47         1.12        58.88        36.76       118.65         8.28 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 
       12.36         1.32        14.50         1.81        12.66        14.89 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ 
       12.59        45.96         1.51         2.24         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3NI 
        0.03         6.94         6.12         1.22        23.84         1.45 
TCGA-FU-A3WB TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LH TCGA-IR-A3LK 
        0.82         9.01        21.67       137.16        78.71        26.56 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A7HU TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73Q 
       15.58         5.13         0.20         2.96         3.39         5.88 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EC TCGA-VS-A8EL 
       10.39        19.59         3.88        11.67        34.52        53.52 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z 
       23.28        49.55        39.78         4.73        23.24 

$`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       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR 
       60.69         9.34         8.35        75.78        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        6.12        20.91        50.76        44.94        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88         2.66       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       17.52         0.76         1.74         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E 
        1.18        14.50         1.35         1.35        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        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
       13.48         0.36        26.27         6.64         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK 
        0.03         0.36         1.18        23.70         0.10         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG 
       20.35         7.92        14.70        19.79         4.73         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-HG-A9SC 
        1.35         1.32         1.97         1.12        25.41         7.13 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93         9.44       147.39        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       96.95        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       21.44        20.48        10.06         6.71        21.11       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       30.31         7.99        11.28         0.89         0.07         0.30 
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-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        4.34         5.49        15.58        13.35        15.95        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PF TCGA-UC-A7PG 
       17.56        14.07        15.88         6.25        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       61.28        10.03        29.03        20.22        14.07        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A952 
       32.15        46.03        11.51        31.27        16.64        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           137.16            195.85 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           14.890            16.015 
[1] "0.0 - 137.2 (14.9)" "0.0 - 195.8 (16.0)"
[1] "hr=" "1.4"
D55V2, continuous
                   vv
clus                T1 T2 T3+T4
  8P LOSS MUTATED   31 15     2
  8P LOSS WILD-TYPE 90 35     9
D55V3, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                 31                90
  T2                 15                35
  T3+T4               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   30 13
  8P LOSS WILD-TYPE 81 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     30   13
  8P LOSS WILD-TYPE   81   34
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              30                81
  1              13                34
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED   27  0 24
  8P LOSS WILD-TYPE 64  8 69
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              27                64
  M1               0                 8
  MX              24                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED               2                               58
  8P LOSS WILD-TYPE             3                              139
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8P LOSS MUTATED                                               0
  8P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8P LOSS MUTATED                                     4
  8P LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8P LOSS MUTATED                                           2
  8P LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8P LOSS MUTATED                                              2
  8P LOSS WILD-TYPE                                            4
D55V6, multiclass
                                               clus
vv                                              8P LOSS MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           58
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              8P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 3
  CERVICAL SQUAMOUS CELL CARCINOMA                            139
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  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"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    12  56
  8P LOSS WILD-TYPE  18 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12   56
  8P LOSS WILD-TYPE   18  152
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               12                18
  YES              56               152
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  3     2
  8P LOSS WILD-TYPE                                5    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED                          10
  8P LOSS WILD-TYPE                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1    49
  8P LOSS WILD-TYPE                                         0   120
D55V10, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 5
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                              10                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  49               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"
D55V11, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4  40
  8P LOSS WILD-TYPE  12 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4   40
  8P LOSS WILD-TYPE   12  109
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                12
  NOT HISPANIC OR LATINO              40               109
[1] 2 2
[1] FALSE
D55V12, continuous
D55V13, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   18 10
  8P LOSS WILD-TYPE 53 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     18   10
  8P LOSS WILD-TYPE   53   15
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  TUMOR FREE              18                53
  WITH TUMOR              10                15
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  8P LOSS MUTATED        7      2       1      3       2            51       2
  8P LOSS WILD-TYPE     16      3       0      7       5           127      12
D55V14, multiclass
               clus
vv              8P LOSS MUTATED 8P LOSS WILD-TYPE
  BRAZIL                      7                16
  CANADA                      2                 3
  NIGERIA                     1                 0
  RUSSIA                      3                 7
  UKRAINE                     2                 5
  UNITED STATES              51               127
  VIETNAM                     2                12
[1] 7 2
[1] 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 26 31  1  6
  8P LOSS WILD-TYPE 14 80 66  0  8
D55V15, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  G1               3                14
  G2              26                80
  G3              31                66
  G4               1                 0
  GX               6                 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"
D55V16, continuous
D55V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8P LOSS MUTATED                                            12
  8P LOSS WILD-TYPE                                          19
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8P LOSS MUTATED               14                  26
  8P LOSS WILD-TYPE             38                  86
D55V18, multiclass
                                                 clus
vv                                                8P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               14
  LIFELONG NON-SMOKER                                          26
                                                 clus
vv                                                8P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 38
  LIFELONG NON-SMOKER                                            86
[1] 5 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
D55V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  8P LOSS MUTATED             6       24             7        1
  8P LOSS WILD-TYPE          13       51             5       11
D55V21, multiclass
               clus
vv              8P LOSS MUTATED 8P LOSS WILD-TYPE
  COMBINATION                 6                13
  EXTERNAL                   24                51
  EXTERNAL BEAM               7                 5
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V22, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    9  2
  8P LOSS WILD-TYPE 16  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      9    2
  8P LOSS WILD-TYPE   16    1
                         clus
vv                        8P LOSS MUTATED 8P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  8P LOSS MUTATED                    0                1                  10
  8P LOSS WILD-TYPE                  2                1                  18
                   vv
clus                REGIONAL SITE
  8P LOSS MUTATED               2
  8P LOSS WILD-TYPE            14
D55V23, multiclass
                     clus
vv                    8P LOSS MUTATED 8P LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD              10                18
  REGIONAL SITE                     2                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V24, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   10  1
  8P LOSS WILD-TYPE 24  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     10    1
  8P LOSS WILD-TYPE   24    2
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  CGY              10                24
  GY                1                 2
[1] 2 2
[1] FALSE
D55V25, continuous
D55V26, continuous
D55V27, continuous
D55V28, continuous
D55V29, continuous
D55V30, 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                      12
  8P LOSS WILD-TYPE                                   5                      17
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8P LOSS MUTATED                         0                       3
  8P LOSS WILD-TYPE                       1                       4
D55V31, multiclass
                                     clus
vv                                    8P LOSS MUTATED 8P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                          12                17
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 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 LOSS MUTATED                                               1
  8P LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8P LOSS MUTATED                                                3
  8P LOSS WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8P LOSS MUTATED                                                                                  18
  8P LOSS WILD-TYPE                                                                                50
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8P LOSS MUTATED                                                                                             32
  8P LOSS WILD-TYPE                                                                                           73
D55V32, multiclass
                                                                                              clus
vv                                                                                             8P 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)                         18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              32
                                                                                              clus
vv                                                                                             8P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           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"
D55V33, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   21 14
  8P LOSS WILD-TYPE 47 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     21   14
  8P LOSS WILD-TYPE   47   56
         clus
vv        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ABSENT               21                47
  PRESENT              14                56
[1] 2 2
[1] FALSE
D55V34, continuous
D55V35, continuous
D55V36, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   13 27
  8P LOSS WILD-TYPE 30 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     13   27
  8P LOSS WILD-TYPE   30   67
                                          clus
vv                                         8P LOSS MUTATED 8P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  13                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              27                67
[1] 2 2
[1] FALSE
D55V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8P LOSS MUTATED              3          14         15
  8P LOSS WILD-TYPE            7          35         42
D55V38, multiclass
              clus
vv             8P LOSS MUTATED 8P LOSS WILD-TYPE
  CURRENT USER               3                 7
  FORMER USER               14                35
  NEVER USED                15                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V39, continuous
D55V40, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   26  4
  8P LOSS WILD-TYPE 63 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     26    4
  8P LOSS WILD-TYPE   63   12
         clus
vv        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ABSENT               26                63
  PRESENT               4                12
[1] 2 2
[1] FALSE
D55V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  8P LOSS MUTATED     0    0  11   16    4  1   2    4    3   5  0   2  0   0
  8P LOSS WILD-TYPE   1    1  19   49   20  3   6    3    6  17  1   6  2   1
                   vv
clus                TX
  8P LOSS MUTATED    5
  8P LOSS WILD-TYPE  9
D55V42, multiclass
      clus
vv     8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B               11                19
  T1B1              16                49
  T1B2               4                20
  T2                 1                 3
  T2A                2                 6
  T2A1               4                 3
  T2A2               3                 6
  T2B                5                17
  T3                 0                 1
  T3B                2                 6
  T4                 0                 2
  TIS                0                 1
  TX                 5                 9
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  8P LOSS MUTATED         2        0         0         1        9        19
  8P LOSS WILD-TYPE       2        2         1         0       22        50
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  8P LOSS MUTATED           6        2         1          4          2
  8P LOSS WILD-TYPE        26        1         5          1          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  8P LOSS MUTATED          10         0          9         0         1
  8P LOSS WILD-TYPE        17         1         25         3         6
D55V44, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                 9                22
  STAGE IB1               19                50
  STAGE IB2                6                26
  STAGE II                 2                 1
  STAGE IIA                1                 5
  STAGE IIA1               4                 1
  STAGE IIA2               2                 5
  STAGE IIB               10                17
  STAGE III                0                 1
  STAGE IIIB               9                25
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    14   5
  8Q LOSS WILD-TYPE 169  45
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               19               214 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                45 
$`8Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT 
       31.40        35.01        57.73        20.91        40.93        73.18 
TCGA-C5-A7X8 TCGA-DG-A2KH TCGA-DS-A0VN TCGA-EA-A439 TCGA-EA-A43B TCGA-EK-A2RM 
        2.73         1.12       118.65        14.50         1.81         2.24 
TCGA-EK-A3GJ TCGA-EX-A3L1 TCGA-LP-A7HU TCGA-PN-A8MA TCGA-UC-A7PD TCGA-VS-A8EL 
        0.10         6.94         0.20         2.96        11.67        53.52 
TCGA-VS-A8QA 
       23.28 

$`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       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
       60.69        94.95         9.34        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35        75.78        99.91        23.51        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91         4.47        58.88        50.76        44.94        40.04 
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        17.52         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-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-A5ZF 
       14.89         1.48        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       13.58        13.48         0.36        12.59        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64         1.51         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         0.07         4.04         0.03         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-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
       20.35         7.92        14.70        19.79         6.12         4.73 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
        1.32         1.97         1.12         9.01        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        10.06         5.13         6.71        21.11       195.85 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       30.31         7.99        11.28         0.89         0.07         0.30 
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-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         5.49        15.58        13.35        15.95         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         5.88         6.25 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       10.39        19.59         3.88        93.99        12.16        61.28 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        34.52        29.03        20.22        14.07        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        46.03        11.51        49.55        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.10              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           118.65            195.85 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           14.500            15.915 
[1] "0.1 - 118.7 (14.5)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.3"
D56V2, continuous
                   vv
clus                 T1  T2 T3+T4
  8Q LOSS MUTATED     8   6     1
  8Q LOSS WILD-TYPE 113  44    10
D56V3, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                  8               113
  T2                  6                44
  T3+T4               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED   12  2
  8Q LOSS WILD-TYPE 99 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     12    2
  8Q LOSS WILD-TYPE   99   45
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              12                99
  1               2                45
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8Q LOSS MUTATED   13  0  1
  8Q LOSS WILD-TYPE 78  8 92
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              13                78
  M1               0                 8
  MX               1                92
[1] 3 2
[1] 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               1                               14
  8Q LOSS WILD-TYPE             4                              183
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8Q LOSS MUTATED                                               0
  8Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8Q LOSS MUTATED                                     4
  8Q LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8Q LOSS MUTATED                                           0
  8Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8Q LOSS MUTATED                                              1
  8Q LOSS WILD-TYPE                                            5
D56V6, multiclass
                                               clus
vv                                              8Q LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           14
  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                                              8Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            183
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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     6  14
  8Q LOSS WILD-TYPE  24 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   14
  8Q LOSS WILD-TYPE   24  194
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                6                24
  YES              14               194
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     2
  8Q LOSS WILD-TYPE                                7    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED                           2
  8Q LOSS WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           1    12
  8Q LOSS WILD-TYPE                                         0   157
D56V10, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               2                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  12               157
[1] 5 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  15 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   12
  8Q LOSS WILD-TYPE   15  137
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              12               137
[1] 2 2
[1] FALSE
D56V12, continuous
D56V13, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    5  3
  8Q LOSS WILD-TYPE 66 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    3
  8Q LOSS WILD-TYPE   66   22
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  TUMOR FREE               5                66
  WITH TUMOR               3                22
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  8Q LOSS MUTATED        2      1       1      0       1            13       2
  8Q LOSS WILD-TYPE     21      4       0     10       6           165      12
D56V14, multiclass
               clus
vv              8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  BRAZIL                      2                21
  CANADA                      1                 4
  NIGERIA                     1                 0
  RUSSIA                      0                10
  UKRAINE                     1                 6
  UNITED STATES              13               165
  VIETNAM                     2                12
[1] 7 2
[1] 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  11   0   2
  8Q LOSS WILD-TYPE  16 100  86   1  12
D56V15, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  G1               1                16
  G2               6               100
  G3              11                86
  G4               0                 1
  GX               2                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"
D56V16, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                33 
       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-C5-A8XH        TCGA-C5-A907 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA        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-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-VS-A8QF        TCGA-VS-A94Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-WL-A834 
"8Q LOSS WILD-TYPE" 
D56V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8Q LOSS MUTATED                                             2
  8Q LOSS WILD-TYPE                                          29
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8Q LOSS MUTATED                5                  10
  8Q LOSS WILD-TYPE             47                 102
D56V18, multiclass
                                                 clus
vv                                                8Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                5
  LIFELONG NON-SMOKER                                          10
                                                 clus
vv                                                8Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 47
  LIFELONG NON-SMOKER                                           102
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V19, continuous
D56V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  8Q LOSS MUTATED             3        5             3        1
  8Q LOSS WILD-TYPE          16       70             9       11
D56V21, multiclass
               clus
vv              8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COMBINATION                 3                16
  EXTERNAL                    5                70
  EXTERNAL BEAM               3                 9
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V22, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    5  0
  8Q LOSS WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    0
  8Q LOSS WILD-TYPE   20    3
                         clus
vv                        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  8Q LOSS MUTATED                    0                0                   2
  8Q LOSS WILD-TYPE                  2                2                  26
                   vv
clus                REGIONAL SITE
  8Q LOSS MUTATED               0
  8Q LOSS WILD-TYPE            16
D56V23, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                46 
       TCGA-C5-A0TN        TCGA-C5-A1BF        TCGA-C5-A1BQ        TCGA-C5-A2LZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CM        TCGA-C5-A7CO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A8XJ        TCGA-C5-A8XK        TCGA-C5-A8YQ        TCGA-C5-A8YT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A8ZZ        TCGA-C5-A907        TCGA-DG-A2KL        TCGA-DS-A7WF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-HM-A3JJ        TCGA-HM-A4S6        TCGA-IR-A3LF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JW-A5VG        TCGA-JX-A5QV        TCGA-MY-A913 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-R2-A69V        TCGA-UC-A7PG        TCGA-VS-A8EC        TCGA-VS-A8EG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-VS-A8EH        TCGA-VS-A8EI        TCGA-VS-A8Q8        TCGA-VS-A8Q9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-VS-A8QC        TCGA-VS-A8QF        TCGA-VS-A8QH        TCGA-VS-A94X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-VS-A94Z        TCGA-VS-A954        TCGA-VS-A957        TCGA-VS-A958 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-VS-A959        TCGA-VS-A9U5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D56V24, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  0
  8Q LOSS WILD-TYPE 32  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    0
  8Q LOSS WILD-TYPE   32    3
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CGY               2                32
  GY                0                 3
[1] 2 2
[1] FALSE
D56V25, continuous
D56V26, continuous
D56V27, continuous
D56V28, continuous
D56V29, continuous
D56V30, 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                       6
  8Q LOSS WILD-TYPE                                   6                      23
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8Q LOSS MUTATED                         0                       1
  8Q LOSS WILD-TYPE                       1                       6
D56V31, multiclass
                                     clus
vv                                    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           6                23
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             15
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8Q LOSS MUTATED                                                                                   4
  8Q LOSS WILD-TYPE                                                                                64
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8Q LOSS MUTATED                                                                                             12
  8Q LOSS WILD-TYPE                                                                                           93
D56V32, 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)                          4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              12
                                                                                              clus
vv                                                                                             8Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V33, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    8  5
  8Q LOSS WILD-TYPE 60 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8    5
  8Q LOSS WILD-TYPE   60   65
         clus
vv        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ABSENT                8                60
  PRESENT               5                65
[1] 2 2
[1] FALSE
D56V34, continuous
D56V35, continuous
D56V36, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6  3
  8Q LOSS WILD-TYPE 37 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6    3
  8Q LOSS WILD-TYPE   37   91
                                          clus
vv                                         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               3                91
[1] 2 2
[1] FALSE
D56V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8Q LOSS MUTATED              2           8          2
  8Q LOSS WILD-TYPE            8          41         55
D56V38, multiclass
              clus
vv             8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CURRENT USER               2                 8
  FORMER USER                8                41
  NEVER USED                 2                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"
D56V39, continuous
D56V40, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    9  1
  8Q LOSS WILD-TYPE 80 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9    1
  8Q LOSS WILD-TYPE   80   15
         clus
vv        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ABSENT                9                80
  PRESENT               1                15
[1] 2 2
[1] FALSE
D56V41, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                11 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MP        TCGA-EK-A2RO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852        TCGA-JX-A3Q8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  8Q LOSS MUTATED     0    0   2    5    1  1   1    2    0   2  0   1  0   0
  8Q LOSS WILD-TYPE   1    1  28   60   23  3   7    5    9  20  1   7  2   1
                   vv
clus                TX
  8Q LOSS MUTATED    0
  8Q LOSS WILD-TYPE 14
D56V42, multiclass
      clus
vv     8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                2                28
  T1B1               5                60
  T1B2               1                23
  T2                 1                 3
  T2A                1                 7
  T2A1               2                 5
  T2A2               0                 9
  T2B                2                20
  T3                 0                 1
  T3B                1                 7
  T4                 0                 2
  TIS                0                 1
  TX                 0                14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  8Q LOSS MUTATED         0        0         0         0        4         7
  8Q LOSS WILD-TYPE       4        2         1         1       27        62
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  8Q LOSS MUTATED           1        1         1          2          0
  8Q LOSS WILD-TYPE        31        2         5          3          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  8Q LOSS MUTATED           3         0          1         0         0
  8Q LOSS WILD-TYPE        24         1         33         3         7
D56V44, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                27
  STAGE IB1                7                62
  STAGE IB2                1                31
  STAGE II                 1                 2
  STAGE IIA                1                 5
  STAGE IIA1               2                 3
  STAGE IIA2               0                 7
  STAGE IIB                3                24
  STAGE III                0                 1
  STAGE IIIB               1                33
  STAGE IVA                0                 3
  STAGE IVB                0                 7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    31  13
  9P LOSS WILD-TYPE 152  37
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               44               189 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               13                37 
$`9P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BJ TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI 
       23.67       144.16        31.40        35.01        57.73        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
        0.46        40.93       154.32        60.69         9.34        13.61 
TCGA-C5-A8YQ TCGA-DG-A2KJ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 
       23.51        58.88         0.76        12.36         1.32         1.35 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PL 
        1.81        12.66         0.36        12.59         1.51         0.43 
TCGA-EK-A2PM TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EX-A69M TCGA-FU-A3YQ TCGA-HM-A3JJ 
        0.59         0.36         2.24         6.12         3.52        21.67 
TCGA-LP-A4AW TCGA-MU-A5YI TCGA-MY-A5BD TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        0.89         0.03        29.72        15.58        13.35         3.39 
TCGA-Q1-A73S TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 
       10.39        10.03        34.52        14.07        19.96        46.03 
TCGA-VS-A8QF TCGA-VS-A959 
       49.55        39.35 

$`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-A1ML 
       46.32        30.21        53.16        38.99         2.43        20.91 
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-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A7XC 
      147.35        17.19        85.55        94.95         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35        75.78        99.91        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91         4.47         1.12        50.76        44.94        40.04 
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-A3HQ 
       22.98        16.83        16.18        17.52         8.28         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-A439 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50        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 
       15.02        14.99        14.96        13.58        13.48        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
       26.27         6.64         0.59         1.45         0.13        16.08 
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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70        19.79         4.73         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-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         1.35         1.32         1.97         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        9.01        25.41         7.13        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX 
       21.11       195.85        30.31         7.99        11.28         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BE 
        0.30         0.82         0.20        13.87         5.42         0.07 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         5.49         2.96        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
       14.07        15.88         5.88         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH 
       11.67        93.99        12.16        61.28        29.03        20.22 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       53.52        32.15        23.28        11.51        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        38.96        18.05 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.03              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           154.32            195.85 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           13.005            16.180 
[1] "0.0 - 154.3 (13.0)" "0.0 - 195.8 (16.2)"
[1] "hr=" "1.8"
D57V2, continuous
                   vv
clus                 T1  T2 T3+T4
  9P LOSS MUTATED    18   6     4
  9P LOSS WILD-TYPE 103  44     7
D57V3, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                 18               103
  T2                  6                44
  T3+T4               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   16  6
  9P LOSS WILD-TYPE 95 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     16    6
  9P LOSS WILD-TYPE   95   41
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              16                95
  1               6                41
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   18  2 12
  9P LOSS WILD-TYPE 73  6 81
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              18                73
  M1               2                 6
  MX              12                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED               1                               40
  9P LOSS WILD-TYPE             4                              157
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9P LOSS MUTATED                                               0
  9P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9P LOSS MUTATED                                     3
  9P LOSS WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9P LOSS MUTATED                                           0
  9P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9P LOSS MUTATED                                              1
  9P LOSS WILD-TYPE                                            5
D57V6, multiclass
                                               clus
vv                                              9P LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           40
  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                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            157
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  5
[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  39
  9P LOSS WILD-TYPE  24 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6   39
  9P LOSS WILD-TYPE   24  169
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                6                24
  YES              39               169
[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                                8    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED                           5
  9P LOSS WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           0    36
  9P LOSS WILD-TYPE                                         1   133
D57V10, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               5                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  36               133
[1] 5 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  29
  9P LOSS WILD-TYPE  15 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   29
  9P LOSS WILD-TYPE   15  120
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              29               120
[1] 2 2
[1] FALSE
D57V12, continuous
D57V13, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   11  6
  9P LOSS WILD-TYPE 60 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     11    6
  9P LOSS WILD-TYPE   60   19
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  TUMOR FREE              11                60
  WITH TUMOR               6                19
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  9P LOSS MUTATED        7      1       0      4       3            28       2
  9P LOSS WILD-TYPE     16      4       1      6       4           150      12
D57V14, multiclass
               clus
vv              9P LOSS MUTATED 9P LOSS WILD-TYPE
  BRAZIL                      7                16
  CANADA                      1                 4
  NIGERIA                     0                 1
  RUSSIA                      4                 6
  UKRAINE                     3                 4
  UNITED STATES              28               150
  VIETNAM                     2                12
[1] 7 2
[1] 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 23 14  0  3
  9P LOSS WILD-TYPE 13 83 83  1 11
D57V15, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  G1               4                13
  G2              23                83
  G3              14                83
  G4               0                 1
  GX               3                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"
D57V16, continuous
D57V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9P LOSS MUTATED                                             5
  9P LOSS WILD-TYPE                                          26
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9P LOSS MUTATED                5                  23
  9P LOSS WILD-TYPE             47                  89
D57V18, multiclass
                                                 clus
vv                                                9P 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                                                5
  LIFELONG NON-SMOKER                                          23
                                                 clus
vv                                                9P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 47
  LIFELONG NON-SMOKER                                            89
[1] 5 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
D57V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  9P LOSS MUTATED             4       14             2        1
  9P LOSS WILD-TYPE          15       61            10       11
D57V21, multiclass
               clus
vv              9P LOSS MUTATED 9P LOSS WILD-TYPE
  COMBINATION                 4                15
  EXTERNAL                   14                61
  EXTERNAL BEAM               2                10
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V22, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    6  0
  9P LOSS WILD-TYPE 19  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    0
  9P LOSS WILD-TYPE   19    3
                         clus
vv                        9P LOSS MUTATED 9P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  6                19
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  9P LOSS MUTATED                    0                1                   5
  9P LOSS WILD-TYPE                  2                1                  23
                   vv
clus                REGIONAL SITE
  9P LOSS MUTATED               4
  9P LOSS WILD-TYPE            12
D57V23, multiclass
                     clus
vv                    9P LOSS MUTATED 9P LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               5                23
  REGIONAL SITE                     4                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V24, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    7  0
  9P LOSS WILD-TYPE 27  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7    0
  9P LOSS WILD-TYPE   27    3
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  CGY               7                27
  GY                0                 3
[1] 2 2
[1] FALSE
D57V25, continuous
D57V26, continuous
D57V27, continuous
D57V28, continuous
D57V29, continuous
D57V30, 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                       3
  9P LOSS WILD-TYPE                                   5                      26
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9P LOSS MUTATED                         0                       0
  9P LOSS WILD-TYPE                       1                       7
D57V31, multiclass
                                     clus
vv                                    9P LOSS MUTATED 9P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           3                26
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  9P LOSS MUTATED                                               0
  9P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9P LOSS MUTATED                                                3
  9P LOSS WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9P LOSS MUTATED                                                                                  18
  9P LOSS WILD-TYPE                                                                                50
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9P LOSS MUTATED                                                                                             15
  9P LOSS WILD-TYPE                                                                                           90
D57V32, multiclass
                                                                                              clus
vv                                                                                             9P 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)                         18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              15
                                                                                              clus
vv                                                                                             9P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           50
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V33, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    8 10
  9P LOSS WILD-TYPE 60 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8   10
  9P LOSS WILD-TYPE   60   60
         clus
vv        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ABSENT                8                60
  PRESENT              10                60
[1] 2 2
[1] FALSE
D57V34, continuous
D57V35, continuous
D57V36, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    7 19
  9P LOSS WILD-TYPE 36 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7   19
  9P LOSS WILD-TYPE   36   75
                                          clus
vv                                         9P LOSS MUTATED 9P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              19                75
[1] 2 2
[1] FALSE
D57V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9P LOSS MUTATED              1          11         11
  9P LOSS WILD-TYPE            9          38         46
D57V38, multiclass
              clus
vv             9P LOSS MUTATED 9P LOSS WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER               11                38
  NEVER USED                11                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"
D57V39, continuous
D57V40, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   13  3
  9P LOSS WILD-TYPE 76 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     13    3
  9P LOSS WILD-TYPE   76   13
         clus
vv        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ABSENT               13                76
  PRESENT               3                13
[1] 2 2
[1] FALSE
D57V41, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"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 T3 T3B T4 TIS
  9P LOSS MUTATED     0    1   4   11    2  0   1    0    2   3  0   4  0   0
  9P LOSS WILD-TYPE   1    0  26   54   22  4   7    7    7  19  1   4  2   1
                   vv
clus                TX
  9P LOSS MUTATED    4
  9P LOSS WILD-TYPE 10
D57V42, multiclass
      clus
vv     9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1A                0                 1
  T1A1               1                 0
  T1B                4                26
  T1B1              11                54
  T1B2               2                22
  T2                 0                 4
  T2A                1                 7
  T2A1               0                 7
  T2A2               2                 7
  T2B                3                19
  T3                 0                 1
  T3B                4                 4
  T4                 0                 2
  TIS                0                 1
  TX                 4                10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  9P LOSS MUTATED         1        1         1         0        3        14
  9P LOSS WILD-TYPE       3        1         0         1       28        55
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  9P LOSS MUTATED           2        1         1          0          0
  9P LOSS WILD-TYPE        30        2         5          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  9P LOSS MUTATED           9         0          9         0         1
  9P LOSS WILD-TYPE        18         1         25         3         6
D57V44, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 1                 1
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                 3                28
  STAGE IB1               14                55
  STAGE IB2                2                30
  STAGE II                 1                 2
  STAGE IIA                1                 5
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                9                18
  STAGE III                0                 1
  STAGE IIIB               9                25
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    26  12
  9Q LOSS WILD-TYPE 157  38
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               38               195 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                38 
$`9Q LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ 
       23.67        31.40        35.01        57.73        35.61         0.46 
TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8YQ 
      154.32        60.69         9.34        13.61         2.73        23.51 
TCGA-DG-A2KJ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A97N 
       58.88         0.76        12.36         1.35         1.81         0.36 
TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EX-A69M 
       12.59         1.51         0.43         0.36         2.24         6.12 
TCGA-HM-A3JJ TCGA-IR-A3LF TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-MU-A5YI TCGA-MY-A5BD 
       21.67        96.95        21.11        30.31         0.03        29.72 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EJ 
        2.96        15.58        13.35        10.03        34.52        19.96 
TCGA-VS-A8QF TCGA-VS-A959 
       49.55        39.35 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43         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-A7UI 
       15.48        20.35       147.35        17.19        85.55        94.95 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR 
       50.99        45.83         8.35        75.78        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
        6.12        20.91         4.47         1.12        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        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        17.52         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-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         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        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PM 
       13.58        13.48        45.96        26.27         6.64         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         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-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-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         4.73         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-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41         7.13        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81       117.40        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58        10.06         5.13         6.71       195.85         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89         0.07         0.30         0.82         0.20 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R3 
       13.87         5.42         0.07         4.34         5.49        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        3.39        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        10.39        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL 
       12.16        61.28        29.03        20.22        14.07        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        46.03        23.28        11.51        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       16.64         4.73        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        38.96        18.05 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.03              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           154.32            195.85 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           14.595            15.950 
[1] "0.0 - 154.3 (14.6)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.9"
D58V2, continuous
                   vv
clus                 T1  T2 T3+T4
  9Q LOSS MUTATED    17   6     3
  9Q LOSS WILD-TYPE 104  44     8
D58V3, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                 17               104
  T2                  6                44
  T3+T4               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   16  5
  9Q LOSS WILD-TYPE 95 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16    5
  9Q LOSS WILD-TYPE   95   42
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              16                95
  1               5                42
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   17  2  9
  9Q LOSS WILD-TYPE 74  6 84
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              17                74
  M1               2                 6
  MX               9                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED               0                               31
  9Q LOSS WILD-TYPE             5                              166
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9Q LOSS MUTATED                                               1
  9Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9Q LOSS MUTATED                                     5
  9Q LOSS WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9Q LOSS MUTATED                                           0
  9Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9Q LOSS MUTATED                                              2
  9Q LOSS WILD-TYPE                                            4
D58V6, multiclass
                                               clus
vv                                              9Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           31
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              9Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            166
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  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"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     4  35
  9Q LOSS WILD-TYPE  26 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4   35
  9Q LOSS WILD-TYPE   26  173
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                4                26
  YES              35               173
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     1
  9Q LOSS WILD-TYPE                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED                           6
  9Q LOSS WILD-TYPE                        18
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           0    30
  9Q LOSS WILD-TYPE                                         1   139
D58V10, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               6                18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  30               139
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  24
  9Q LOSS WILD-TYPE  14 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   24
  9Q LOSS WILD-TYPE   14  125
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              24               125
[1] 2 2
[1] FALSE
D58V12, continuous
D58V13, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   10  5
  9Q LOSS WILD-TYPE 61 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10    5
  9Q LOSS WILD-TYPE   61   20
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  TUMOR FREE              10                61
  WITH TUMOR               5                20
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  9Q LOSS MUTATED        5      1       1      3       2            27       0
  9Q LOSS WILD-TYPE     18      4       0      7       5           151      14
D58V14, multiclass
               clus
vv              9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  BRAZIL                      5                18
  CANADA                      1                 4
  NIGERIA                     1                 0
  RUSSIA                      3                 7
  UKRAINE                     2                 5
  UNITED STATES              27               151
  VIETNAM                     0                14
[1] 7 2
[1] 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 20 15  0  1
  9Q LOSS WILD-TYPE 15 86 82  1 13
D58V15, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  G1               2                15
  G2              20                86
  G3              15                82
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V16, continuous
D58V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9Q LOSS MUTATED                                             3
  9Q LOSS WILD-TYPE                                          28
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9Q LOSS MUTATED                4                  20
  9Q LOSS WILD-TYPE             48                  92
D58V18, multiclass
                                                 clus
vv                                                9Q 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                                                4
  LIFELONG NON-SMOKER                                          20
                                                 clus
vv                                                9Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 48
  LIFELONG NON-SMOKER                                            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"
D58V19, continuous
D58V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  9Q LOSS MUTATED             2       13             2        1
  9Q LOSS WILD-TYPE          17       62            10       11
D58V21, multiclass
               clus
vv              9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COMBINATION                 2                17
  EXTERNAL                   13                62
  EXTERNAL BEAM               2                10
  INTERNAL                    1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V22, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    4  0
  9Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4    0
  9Q LOSS WILD-TYPE   21    3
                         clus
vv                        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  4                21
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  9Q LOSS MUTATED                    0                1                   4
  9Q LOSS WILD-TYPE                  2                1                  24
                   vv
clus                REGIONAL SITE
  9Q LOSS MUTATED               4
  9Q LOSS WILD-TYPE            12
D58V23, multiclass
                     clus
vv                    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  DISTANT RECURRENCE                0                 2
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               4                24
  REGIONAL SITE                     4                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V24, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6  0
  9Q LOSS WILD-TYPE 28  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    0
  9Q LOSS WILD-TYPE   28    3
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CGY               6                28
  GY                0                 3
[1] 2 2
[1] FALSE
D58V25, continuous
D58V26, continuous
D58V27, continuous
D58V28, continuous
D58V29, continuous
D58V30, 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                       4
  9Q LOSS WILD-TYPE                                   5                      25
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9Q LOSS MUTATED                         0                       0
  9Q LOSS WILD-TYPE                       1                       7
D58V31, multiclass
                                     clus
vv                                    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           4                25
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  9Q LOSS MUTATED                                               0
  9Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9Q LOSS MUTATED                                                2
  9Q LOSS WILD-TYPE                                             14
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9Q LOSS MUTATED                                                                                  16
  9Q LOSS WILD-TYPE                                                                                52
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9Q LOSS MUTATED                                                                                             12
  9Q LOSS WILD-TYPE                                                                                           93
D58V32, multiclass
                                                                                              clus
vv                                                                                             9Q 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)              12
                                                                                              clus
vv                                                                                             9Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           52
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V33, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    9 11
  9Q LOSS WILD-TYPE 59 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9   11
  9Q LOSS WILD-TYPE   59   59
         clus
vv        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ABSENT                9                59
  PRESENT              11                59
[1] 2 2
[1] FALSE
D58V34, continuous
D58V35, continuous
D58V36, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    5 15
  9Q LOSS WILD-TYPE 38 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5   15
  9Q LOSS WILD-TYPE   38   79
                                          clus
vv                                         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              15                79
[1] 2 2
[1] FALSE
D58V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9Q LOSS MUTATED              1          10         10
  9Q LOSS WILD-TYPE            9          39         47
D58V38, multiclass
              clus
vv             9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CURRENT USER               1                 9
  FORMER USER               10                39
  NEVER USED                10                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"
D58V39, continuous
D58V40, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   15  2
  9Q LOSS WILD-TYPE 74 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15    2
  9Q LOSS WILD-TYPE   74   14
         clus
vv        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ABSENT               15                74
  PRESENT               2                14
[1] 2 2
[1] FALSE
D58V41, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                12 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  9Q LOSS MUTATED     0    1   3   11    2  0   1    0    1   4  0   3  0   0
  9Q LOSS WILD-TYPE   1    0  27   54   22  4   7    7    8  18  1   5  2   1
                   vv
clus                TX
  9Q LOSS MUTATED    2
  9Q LOSS WILD-TYPE 12
D58V42, multiclass
      clus
vv     9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1A                0                 1
  T1A1               1                 0
  T1B                3                27
  T1B1              11                54
  T1B2               2                22
  T2                 0                 4
  T2A                1                 7
  T2A1               0                 7
  T2A2               1                 8
  T2B                4                18
  T3                 0                 1
  T3B                3                 5
  T4                 0                 2
  TIS                0                 1
  TX                 2                12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  9Q LOSS MUTATED         0        0         1         0        3        14
  9Q LOSS WILD-TYPE       4        2         0         1       28        55
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  9Q LOSS MUTATED           2        0         2          0          0
  9Q LOSS WILD-TYPE        30        3         4          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  9Q LOSS MUTATED           7         0          7         0         1
  9Q LOSS WILD-TYPE        20         1         27         3         6
D58V44, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 0                 2
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                 3                28
  STAGE IB1               14                55
  STAGE IB2                2                30
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                7                20
  STAGE III                0                 1
  STAGE IIIB               7                27
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    34  14
  10P LOSS WILD-TYPE 149  36
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                48                185 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                 36 
$`10P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1MH 
       23.67        11.44        82.85        19.86        31.40        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV 
       35.61         0.46        20.91        40.93        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7X8 TCGA-C5-A8YR 
       83.05       182.93        20.35       147.35         2.73        27.52 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF 
       58.88        44.94        13.05        14.50        14.89        14.96 
TCGA-EK-A2H1 TCGA-EK-A2PM TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 
       26.27         0.59         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-JX-A3Q8 TCGA-LP-A4AX TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 
       20.48        30.31         0.07         5.49         2.96        13.35 
TCGA-Q1-A6DT TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A94Y TCGA-VS-A954 
        3.39        93.99        12.16        53.52         4.73        42.58 

$`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       154.32       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-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       50.99        45.83         8.35        75.78        99.91        23.51 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM 
        6.12        20.91         4.47         1.12        50.76        40.04 
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        17.52         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        15.02        14.99        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48         0.36        12.59        45.96         6.64         1.51 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.59         1.45         0.13        16.08         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ 
        4.04         0.03         1.18        23.70         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.03         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.12         4.73        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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41         7.13        21.67 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       147.39       137.16       117.40        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        15.58        10.06         5.13         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 
      195.85         7.99        11.28         0.89         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.20        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        4.34        15.58        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         5.88         6.25        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       11.67        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       14.07        19.96        32.15        46.03        23.28        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       49.55        39.78        31.27        16.64        23.24        44.88 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.08        43.82        39.35        38.96        18.05 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            182.93             195.85 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            20.415             15.480 
[1] "0.1 - 182.9 (20.4)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                  T1  T2 T3+T4
  10P LOSS MUTATED    20  14     2
  10P LOSS WILD-TYPE 101  36     9
D59V3, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                  20                101
  T2                  14                 36
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   17 15
  10P LOSS WILD-TYPE 94 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     17   15
  10P LOSS WILD-TYPE   94   32
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               17                 94
  1               15                 32
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED   17  1 20
  10P LOSS WILD-TYPE 74  7 73
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               17                 74
  M1                1                  7
  MX               20                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED               0                               43
  10P LOSS WILD-TYPE             5                              154
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10P LOSS MUTATED                                               1
  10P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10P LOSS MUTATED                                     4
  10P LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10P LOSS MUTATED                                           1
  10P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10P LOSS MUTATED                                              1
  10P LOSS WILD-TYPE                                            5
D59V6, multiclass
                                               clus
vv                                              10P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            43
  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                                              10P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             154
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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    11  39
  10P LOSS WILD-TYPE  19 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     11   39
  10P LOSS WILD-TYPE   19  169
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                11                 19
  YES               39                169
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     4
  10P LOSS WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED                           9
  10P LOSS WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           0    33
  10P LOSS WILD-TYPE                                         1   136
D59V10, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                9                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   33                136
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  31
  10P LOSS WILD-TYPE  14 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   31
  10P LOSS WILD-TYPE   14  118
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               31                118
[1] 2 2
[1] FALSE
D59V12, continuous
D59V13, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   20  7
  10P LOSS WILD-TYPE 51 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20    7
  10P LOSS WILD-TYPE   51   18
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  TUMOR FREE               20                 51
  WITH TUMOR                7                 18
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  10P LOSS MUTATED        3      2       1      1       0            40       3
  10P LOSS WILD-TYPE     20      3       0      9       7           138      11
D59V14, multiclass
               clus
vv              10P LOSS MUTATED 10P LOSS WILD-TYPE
  BRAZIL                       3                 20
  CANADA                       2                  3
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      0                  7
  UNITED STATES               40                138
  VIETNAM                      3                 11
[1] 7 2
[1] 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    2 17 28  1  2
  10P LOSS WILD-TYPE 15 89 69  0 12
D59V15, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  G1                2                 15
  G2               17                 89
  G3               28                 69
  G4                1                  0
  GX                2                 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"
D59V16, continuous
D59V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10P LOSS MUTATED                                             6
  10P LOSS WILD-TYPE                                          25
                    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                                                 1
  10P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10P LOSS MUTATED               13                  16
  10P LOSS WILD-TYPE             39                  96
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                1
  CURRENT SMOKER                                                13
  LIFELONG NON-SMOKER                                           16
                                                 clus
vv                                                10P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  39
  LIFELONG NON-SMOKER                                             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"
D59V19, continuous
D59V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  10P LOSS MUTATED             7       14             3        2
  10P LOSS WILD-TYPE          12       61             9       10
D59V21, multiclass
               clus
vv              10P LOSS MUTATED 10P LOSS WILD-TYPE
  COMBINATION                  7                 12
  EXTERNAL                    14                 61
  EXTERNAL BEAM                3                  9
  INTERNAL                     2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V22, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9  1
  10P LOSS WILD-TYPE 16  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9    1
  10P LOSS WILD-TYPE   16    2
                         clus
vv                        10P LOSS MUTATED 10P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  10P LOSS MUTATED                    0                1                   7
  10P LOSS WILD-TYPE                  2                1                  21
                    vv
clus                 REGIONAL SITE
  10P LOSS MUTATED               2
  10P LOSS WILD-TYPE            14
D59V23, multiclass
                     clus
vv                    10P LOSS MUTATED 10P LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   1                  1
  PRIMARY TUMOR FIELD                7                 21
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V24, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    8  1
  10P LOSS WILD-TYPE 26  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8    1
  10P LOSS WILD-TYPE   26    2
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  CGY                8                 26
  GY                 1                  2
[1] 2 2
[1] FALSE
D59V25, continuous
D59V26, continuous
D59V27, continuous
D59V28, continuous
D59V29, continuous
D59V30, 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                         5                       0
  10P LOSS WILD-TYPE                      24                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10P LOSS MUTATED                         4
  10P LOSS WILD-TYPE                       3
D59V31, multiclass
                                     clus
vv                                    10P LOSS MUTATED 10P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                3                  3
  OTHER LOCATION, SPECIFY                            5                 24
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            4                  3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  10P LOSS MUTATED                                               0
  10P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  10P LOSS MUTATED                                                4
  10P LOSS WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10P LOSS MUTATED                                                                                  19
  10P LOSS WILD-TYPE                                                                                49
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10P LOSS MUTATED                                                                                             19
  10P LOSS WILD-TYPE                                                                                           86
D59V32, 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)                          19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               19
                                                                                              clus
vv                                                                                             10P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V33, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9 19
  10P LOSS WILD-TYPE 59 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9   19
  10P LOSS WILD-TYPE   59   51
         clus
vv        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ABSENT                 9                 59
  PRESENT               19                 51
[1] 2 2
[1] FALSE
D59V34, continuous
D59V35, continuous
D59V36, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   12 17
  10P LOSS WILD-TYPE 31 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     12   17
  10P LOSS WILD-TYPE   31   77
                                          clus
vv                                         10P LOSS MUTATED 10P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   12                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               17                 77
[1] 2 2
[1] FALSE
D59V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10P LOSS MUTATED              2          11          8
  10P LOSS WILD-TYPE            8          38         49
D59V38, multiclass
              clus
vv             10P LOSS MUTATED 10P LOSS WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                11                 38
  NEVER USED                  8                 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"
D59V39, continuous
D59V40, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   16  4
  10P LOSS WILD-TYPE 73 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     16    4
  10P LOSS WILD-TYPE   73   12
         clus
vv        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ABSENT                16                 73
  PRESENT                4                 12
[1] 2 2
[1] FALSE
D59V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  10P LOSS MUTATED     0    0   6   13    1  2   2    3    1   6  0   2  0   1
  10P LOSS WILD-TYPE   1    1  24   52   23  2   6    4    8  16  1   6  2   0
                    vv
clus                 TX
  10P LOSS MUTATED    2
  10P LOSS WILD-TYPE 12
D59V42, multiclass
      clus
vv     10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 6                 24
  T1B1               13                 52
  T1B2                1                 23
  T2                  2                  2
  T2A                 2                  6
  T2A1                3                  4
  T2A2                1                  8
  T2B                 6                 16
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 1                  0
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  10P LOSS MUTATED         1        0         0         1        6        13
  10P LOSS WILD-TYPE       3        2         1         0       25        56
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  10P LOSS MUTATED           6        0         3          2          1
  10P LOSS WILD-TYPE        26        3         3          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  10P LOSS MUTATED           6         0         10         0         0
  10P LOSS WILD-TYPE        21         1         24         3         7
D59V44, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  6                 25
  STAGE IB1                13                 56
  STAGE IB2                 6                 26
  STAGE II                  0                  3
  STAGE IIA                 3                  3
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                 6                 21
  STAGE III                 0                  1
  STAGE IIIB               10                 24
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    41  16
  10Q LOSS WILD-TYPE 142  34
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                57                176 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                16                 34 
$`10Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M6 
       57.04        23.67        11.44        82.85        19.86        31.40 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A2LT TCGA-C5-A2LV 
       38.99        35.61         0.46        20.91        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7X5 TCGA-C5-A7X8 
       83.05       182.93        20.35       147.35        13.61         2.73 
TCGA-C5-A8YR TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VK TCGA-EA-A3QD TCGA-EA-A439 
       27.52        58.88        44.94        36.76        13.05        14.50 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PM 
       14.89        14.96        13.48        12.59        26.27         0.59 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG 
        1.18         2.24         0.10        20.35         1.22         0.92 
TCGA-FU-A3TQ TCGA-FU-A40J TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LB 
        1.58         1.35         9.01        21.67        20.78        66.81 
TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-MY-A913 
       78.71        20.48        10.06        30.31         0.07         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EL 
        2.96        13.35         3.39        12.16        61.28        53.52 
TCGA-VS-A94Y TCGA-VS-A954 TCGA-VS-A9U5 
        4.73        42.58        38.96 

$`10Q 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-A1BN TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
      173.29         5.46        67.46        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       57.73        53.16         2.43        40.93         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       154.32       101.82       134.33        15.48 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC 
       17.19        85.55        60.69        94.95         9.34        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT 
       45.83         8.35        75.78        99.91        23.51         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91         4.47         1.12        50.76        40.04        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88         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        17.52         8.28         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        1.32         0.82         0.62         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35         1.81        12.66        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2H0 
       13.91        15.02        14.99        13.58         0.36        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        6.64         1.51         0.43         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       16.08         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-A3L1 
        0.07         0.10         0.10         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO 
       14.70        19.79         6.12         4.73        23.84         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.45         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41         7.13        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
        9.44       147.39       137.16       117.40        96.95        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       26.56        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58         5.13         6.71        21.11       195.85         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       11.28         0.89         0.30         0.82         0.20        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        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        10.39        19.59         3.88        11.67        93.99 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        34.52        29.03        20.22        14.07        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        23.28        11.51        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 
       31.27        16.64        23.24        44.88        42.08        43.82 
TCGA-VS-A959 TCGA-WL-A834 
       39.35        18.05 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            182.93             195.85 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             20.35              15.58 
[1] "0.1 - 182.9 (20.4)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.4"
D60V2, continuous
                    vv
clus                 T1 T2 T3+T4
  10Q LOSS MUTATED   27 15     2
  10Q LOSS WILD-TYPE 94 35     9
D60V3, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                  27                 94
  T2                  15                 35
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   20 17
  10Q LOSS WILD-TYPE 91 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     20   17
  10Q LOSS WILD-TYPE   91   30
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               20                 91
  1               17                 30
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED   19  1 26
  10Q LOSS WILD-TYPE 72  7 67
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               19                 72
  M1                1                  7
  MX               26                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED               0                               50
  10Q LOSS WILD-TYPE             5                              147
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10Q LOSS MUTATED                                               1
  10Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10Q LOSS MUTATED                                     5
  10Q LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10Q LOSS MUTATED                                           2
  10Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10Q LOSS MUTATED                                              1
  10Q LOSS WILD-TYPE                                            5
D60V6, multiclass
                                               clus
vv                                              10Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              10Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             147
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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    11  48
  10Q LOSS WILD-TYPE  19 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     11   48
  10Q LOSS WILD-TYPE   19  160
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                11                 19
  YES               48                160
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     5
  10Q LOSS WILD-TYPE                                8    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED                          12
  10Q LOSS WILD-TYPE                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           0    39
  10Q LOSS WILD-TYPE                                         1   130
D60V10, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    5                 13
  BLACK OR AFRICAN AMERICAN                               12                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   39                130
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3  39
  10Q LOSS WILD-TYPE  13 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   39
  10Q LOSS WILD-TYPE   13  110
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               39                110
[1] 2 2
[1] FALSE
D60V12, continuous
D60V13, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   21  9
  10Q LOSS WILD-TYPE 50 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21    9
  10Q LOSS WILD-TYPE   50   16
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  TUMOR FREE               21                 50
  WITH TUMOR                9                 16
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  10Q LOSS MUTATED        4      2       1      1       0            47       4
  10Q LOSS WILD-TYPE     19      3       0      9       7           131      10
D60V14, multiclass
               clus
vv              10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  BRAZIL                       4                 19
  CANADA                       2                  3
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      0                  7
  UNITED STATES               47                131
  VIETNAM                      4                 10
[1] 7 2
[1] 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    3 17 35  1  3
  10Q LOSS WILD-TYPE 14 89 62  0 11
D60V15, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  G1                3                 14
  G2               17                 89
  G3               35                 62
  G4                1                  0
  GX                3                 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"
D60V16, continuous
D60V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10Q LOSS MUTATED                                             7
  10Q LOSS WILD-TYPE                                          24
                    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                                                 1
  10Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10Q LOSS MUTATED               14                  20
  10Q LOSS WILD-TYPE             38                  92
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                1
  CURRENT SMOKER                                                14
  LIFELONG NON-SMOKER                                           20
                                                 clus
vv                                                10Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  38
  LIFELONG NON-SMOKER                                             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"
D60V19, continuous
D60V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  10Q LOSS MUTATED             6       17             5        2
  10Q LOSS WILD-TYPE          13       58             7       10
D60V21, multiclass
               clus
vv              10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COMBINATION                  6                 13
  EXTERNAL                    17                 58
  EXTERNAL BEAM                5                  7
  INTERNAL                     2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V22, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    9  1
  10Q LOSS WILD-TYPE 16  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9    1
  10Q LOSS WILD-TYPE   16    2
                         clus
vv                        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  10Q LOSS MUTATED                    0                2                   9
  10Q LOSS WILD-TYPE                  2                0                  19
                    vv
clus                 REGIONAL SITE
  10Q LOSS MUTATED               2
  10Q LOSS WILD-TYPE            14
D60V23, multiclass
                     clus
vv                    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   2                  0
  PRIMARY TUMOR FIELD                9                 19
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V24, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   10  1
  10Q LOSS WILD-TYPE 24  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     10    1
  10Q LOSS WILD-TYPE   24    2
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CGY               10                 24
  GY                 1                  2
[1] 2 2
[1] FALSE
D60V25, continuous
D60V26, continuous
D60V27, continuous
D60V28, continuous
D60V29, continuous
D60V30, 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                         5                       0
  10Q LOSS WILD-TYPE                      24                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10Q LOSS MUTATED                         5
  10Q LOSS WILD-TYPE                       2
D60V31, multiclass
                                     clus
vv                                    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                3                  3
  OTHER LOCATION, SPECIFY                            5                 24
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            5                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  10Q LOSS MUTATED                                               0
  10Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  10Q LOSS MUTATED                                                6
  10Q LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10Q LOSS MUTATED                                                                                  21
  10Q LOSS WILD-TYPE                                                                                47
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10Q LOSS MUTATED                                                                                             21
  10Q LOSS WILD-TYPE                                                                                           84
D60V32, multiclass
                                                                                              clus
vv                                                                                             10Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               21
                                                                                              clus
vv                                                                                             10Q 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)                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V33, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   12 22
  10Q LOSS WILD-TYPE 56 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     12   22
  10Q LOSS WILD-TYPE   56   48
         clus
vv        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ABSENT                12                 56
  PRESENT               22                 48
[1] 2 2
[1] FALSE
D60V34, continuous
D60V35, continuous
D60V36, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   12 24
  10Q LOSS WILD-TYPE 31 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     12   24
  10Q LOSS WILD-TYPE   31   70
                                          clus
vv                                         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   12                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               24                 70
[1] 2 2
[1] FALSE
D60V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10Q LOSS MUTATED              2          12         11
  10Q LOSS WILD-TYPE            8          37         46
D60V38, multiclass
              clus
vv             10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                12                 37
  NEVER USED                 11                 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"
D60V39, continuous
D60V40, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   19  4
  10Q LOSS WILD-TYPE 70 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     19    4
  10Q LOSS WILD-TYPE   70   12
         clus
vv        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ABSENT                19                 70
  PRESENT                4                 12
[1] 2 2
[1] FALSE
D60V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  10Q LOSS MUTATED     0    0   7   17    3  2   2    3    0   8  0   2  0   1
  10Q LOSS WILD-TYPE   1    1  23   48   21  2   6    4    9  14  1   6  2   0
                    vv
clus                 TX
  10Q LOSS MUTATED    2
  10Q LOSS WILD-TYPE 12
D60V42, multiclass
      clus
vv     10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 7                 23
  T1B1               17                 48
  T1B2                3                 21
  T2                  2                  2
  T2A                 2                  6
  T2A1                3                  4
  T2A2                0                  9
  T2B                 8                 14
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 1                  0
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  10Q LOSS MUTATED         1        0         0         1        8        16
  10Q LOSS WILD-TYPE       3        2         1         0       23        53
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  10Q LOSS MUTATED           8        0         2          2          1
  10Q LOSS WILD-TYPE        24        3         4          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  10Q LOSS MUTATED           7         0         11         0         1
  10Q LOSS WILD-TYPE        20         1         23         3         6
D60V44, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  8                 23
  STAGE IB1                16                 53
  STAGE IB2                 8                 24
  STAGE II                  0                  3
  STAGE IIA                 2                  4
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                 7                 20
  STAGE III                 0                  1
  STAGE IIIB               11                 23
  STAGE IVA                 0                  3
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    56  22
  11P LOSS WILD-TYPE 127  28
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                78                155 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                22                 28 
$`11P LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        18.74       177.04        19.86        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A2LV 
       30.21        38.99        35.61         0.46        20.91        73.45 
TCGA-C5-A2LZ TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A7UI 
      100.14       182.93       154.32        15.48        60.69        94.95 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
        2.73        50.99        75.78        99.91        23.51        27.52 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 
       87.75        36.76       118.65        12.36         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A97N 
        1.81        12.66         0.26        14.99        14.96         0.36 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RM TCGA-EK-A3GJ 
        1.51         0.43         0.59        16.08         2.24         0.10 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-IR-A3LA TCGA-IR-A3LC 
       20.35        23.84         1.45         0.82       137.16       117.40 
TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AX 
       26.56        24.56        21.44        20.48        11.28         0.07 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA 
        0.82         0.20        13.87        29.72         0.07         2.96 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG 
       13.35         3.39         5.88        19.59        11.67        12.16 
TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QC 
       10.03        20.22        14.07        19.96        46.03        11.51 
TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       49.55         4.73        23.24        42.08        39.35        38.96 

$`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-A7CM TCGA-C5-A7CO 
       17.85        20.42       101.82       134.33        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XI 
       17.19        85.55         9.34        13.61        45.83         8.35 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        6.12        20.91         4.47         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       44.94        40.04        58.88         2.66       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18        17.52         8.28         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-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
        1.35        12.82        14.89         1.48        13.91        15.02 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48        12.59        45.96        26.27         6.64 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         1.45         0.13         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK 
        0.36         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        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        4.73         1.22         0.92         2.17         0.66         1.02 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH 
       14.93         9.44       147.39        66.81        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VL TCGA-JW-A69B 
       81.96        36.36        27.42         3.29        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        5.13         6.71        21.11       195.85        30.31         7.99 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF TCGA-MY-A913 
        0.89         0.30         0.03         5.42         4.34         5.49 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC 
        6.25        10.39         3.88        93.99        61.28        34.52 
TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM 
       29.03        53.52        32.15        23.28        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-WL-A834 
       16.64        44.88        42.58        43.82        18.05 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            182.93             195.85 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.91              14.93 
[1] "0.1 - 182.9 (19.9)" "0.0 - 195.8 (14.9)"
[1] "hr=" "1.3"
D61V2, continuous
                    vv
clus                 T1 T2 T3+T4
  11P LOSS MUTATED   33 20     5
  11P LOSS WILD-TYPE 88 30     6
D61V3, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                  33                 88
  T2                  20                 30
  T3+T4                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   35 11
  11P LOSS WILD-TYPE 76 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     35   11
  11P LOSS WILD-TYPE   76   36
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               35                 76
  1               11                 36
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED   31  2 31
  11P LOSS WILD-TYPE 60  6 62
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               31                 60
  M1                2                  6
  MX               31                 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
  11P LOSS MUTATED               0                               76
  11P LOSS WILD-TYPE             5                              121
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11P LOSS MUTATED                                               0
  11P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11P LOSS MUTATED                                     3
  11P LOSS WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11P LOSS MUTATED                                           1
  11P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11P LOSS MUTATED                                              1
  11P LOSS WILD-TYPE                                            5
D61V6, multiclass
                                               clus
vv                                              11P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            76
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              11P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             121
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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     8  73
  11P LOSS WILD-TYPE  22 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8   73
  11P LOSS WILD-TYPE   22  135
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 8                 22
  YES               73                135
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  3    10
  11P LOSS WILD-TYPE                                5     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED                           9
  11P LOSS WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           1    55
  11P LOSS WILD-TYPE                                         0   114
D61V10, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  5
  ASIAN                                                   10                  8
  BLACK OR AFRICAN AMERICAN                                9                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   55                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"
D61V11, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5  47
  11P LOSS WILD-TYPE  11 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5   47
  11P LOSS WILD-TYPE   11  102
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO               47                102
[1] 2 2
[1] FALSE
D61V12, continuous
D61V13, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   18 13
  11P LOSS WILD-TYPE 53 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18   13
  11P LOSS WILD-TYPE   53   12
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  TUMOR FREE               18                 53
  WITH TUMOR               13                 12
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  11P LOSS MUTATED       12      0       1      2       3            54       9
  11P LOSS WILD-TYPE     11      5       0      8       4           124       5
D61V14, multiclass
               clus
vv              11P LOSS MUTATED 11P LOSS WILD-TYPE
  BRAZIL                      12                 11
  CANADA                       0                  5
  NIGERIA                      1                  0
  RUSSIA                       2                  8
  UKRAINE                      3                  4
  UNITED STATES               54                124
  VIETNAM                      9                  5
[1] 7 2
[1] 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    3 32 39  0  5
  11P LOSS WILD-TYPE 14 74 58  1  9
D61V15, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  G1                3                 14
  G2               32                 74
  G3               39                 58
  G4                0                  1
  GX                5                  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"
D61V16, continuous
D61V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11P LOSS MUTATED                                             7
  11P LOSS WILD-TYPE                                          24
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11P LOSS MUTATED               21                  43
  11P LOSS WILD-TYPE             31                  69
D61V18, multiclass
                                                 clus
vv                                                11P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                21
  LIFELONG NON-SMOKER                                           43
                                                 clus
vv                                                11P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  31
  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"
D61V19, continuous
D61V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  11P LOSS MUTATED             5       30             3        3
  11P LOSS WILD-TYPE          14       45             9        9
D61V21, multiclass
               clus
vv              11P LOSS MUTATED 11P LOSS WILD-TYPE
  COMBINATION                  5                 14
  EXTERNAL                    30                 45
  EXTERNAL BEAM                3                  9
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V22, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    7  0
  11P LOSS WILD-TYPE 18  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7    0
  11P LOSS WILD-TYPE   18    3
                         clus
vv                        11P LOSS MUTATED 11P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   7                 18
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  11P LOSS MUTATED                    1                0                  12
  11P LOSS WILD-TYPE                  1                2                  16
                    vv
clus                 REGIONAL SITE
  11P LOSS MUTATED               7
  11P LOSS WILD-TYPE             9
D61V23, multiclass
                     clus
vv                    11P LOSS MUTATED 11P LOSS WILD-TYPE
  DISTANT RECURRENCE                 1                  1
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD               12                 16
  REGIONAL SITE                      7                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V24, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   12  2
  11P LOSS WILD-TYPE 22  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     12    2
  11P LOSS WILD-TYPE   22    1
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  CGY               12                 22
  GY                 2                  1
[1] 2 2
[1] FALSE
D61V25, continuous
D61V26, continuous
D61V27, continuous
D61V28, continuous
D61V29, continuous
D61V30, 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                         8                       1
  11P LOSS WILD-TYPE                      21                       0
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11P LOSS MUTATED                         1
  11P LOSS WILD-TYPE                       6
D61V31, multiclass
                                     clus
vv                                    11P LOSS MUTATED 11P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                            8                 21
  POSITIVE BLADDER MARGIN                            1                  0
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  11P LOSS MUTATED                                               1
  11P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11P LOSS MUTATED                                                8
  11P LOSS WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11P LOSS MUTATED                                                                                  29
  11P LOSS WILD-TYPE                                                                                39
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11P LOSS MUTATED                                                                                             26
  11P LOSS WILD-TYPE                                                                                           79
D61V32, multiclass
                                                                                              clus
vv                                                                                             11P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               26
                                                                                              clus
vv                                                                                             11P 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)                            39
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V33, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   21 16
  11P LOSS WILD-TYPE 47 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     21   16
  11P LOSS WILD-TYPE   47   54
         clus
vv        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ABSENT                21                 47
  PRESENT               16                 54
[1] 2 2
[1] FALSE
D61V34, continuous
D61V35, continuous
D61V36, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   16 29
  11P LOSS WILD-TYPE 27 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     16   29
  11P LOSS WILD-TYPE   27   65
                                          clus
vv                                         11P LOSS MUTATED 11P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   16                 27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               29                 65
[1] 2 2
[1] FALSE
D61V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11P LOSS MUTATED              2          12         24
  11P LOSS WILD-TYPE            8          37         33
D61V38, multiclass
              clus
vv             11P LOSS MUTATED 11P LOSS WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                12                 37
  NEVER USED                 24                 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"
D61V39, continuous
D61V40, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   25  6
  11P LOSS WILD-TYPE 64 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     25    6
  11P LOSS WILD-TYPE   64   10
         clus
vv        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ABSENT                25                 64
  PRESENT                6                 10
[1] 2 2
[1] FALSE
D61V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  11P LOSS MUTATED     1    0  11   17    4  2   1    3    3  11  0   4  1   0
  11P LOSS WILD-TYPE   0    1  19   48   20  2   7    4    6  11  1   4  1   1
                    vv
clus                 TX
  11P LOSS MUTATED    7
  11P LOSS WILD-TYPE  7
D61V42, multiclass
      clus
vv     11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1A                 1                  0
  T1A1                0                  1
  T1B                11                 19
  T1B1               17                 48
  T1B2                4                 20
  T2                  2                  2
  T2A                 1                  7
  T2A1                3                  4
  T2A2                3                  6
  T2B                11                 11
  T3                  0                  1
  T3B                 4                  4
  T4                  1                  1
  TIS                 0                  1
  TX                  7                  7
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  11P LOSS MUTATED         2        1         0         1       15        19
  11P LOSS WILD-TYPE       2        1         1         0       16        50
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  11P LOSS MUTATED           4        1         1          3          2
  11P LOSS WILD-TYPE        28        2         5          2          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  11P LOSS MUTATED          15         0         12         2         0
  11P LOSS WILD-TYPE        12         1         22         1         7
D61V44, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                  1                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                 15                 16
  STAGE IB1                19                 50
  STAGE IB2                 4                 28
  STAGE II                  1                  2
  STAGE IIA                 1                  5
  STAGE IIA1                3                  2
  STAGE IIA2                2                  5
  STAGE IIB                15                 12
  STAGE III                 0                  1
  STAGE IIIB               12                 22
  STAGE IVA                 2                  1
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    66  25
  11Q LOSS WILD-TYPE 117  25
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                91                142 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                25                 25 
$`11Q LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
       49.48        68.84        18.74        31.40        46.32        30.21 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A2LV TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL 
       73.45       100.14         0.82       182.93       154.32        15.48 
TCGA-C5-A7CM TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
       20.35        60.69         2.73        45.83        75.78        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VN 
       23.51        27.52        50.76        87.75        36.76       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-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG 
       14.99        14.96        13.48         0.36        12.59         1.51 
TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EK-A3GJ 
        0.59         0.13        16.08         0.03         2.24         0.10 
TCGA-EX-A1H5 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       20.35        19.79         6.12         1.45         1.58         0.82 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-JW-A5VK TCGA-LP-A4AU 
      137.16        66.81       117.40        81.96        20.48        11.28 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD 
        0.07         0.82         0.20        13.87         0.03        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW 
        0.07         4.34         2.96        13.35         3.39        17.56 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       15.88         5.88        19.59        11.67        93.99        12.16 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        29.03        20.22        14.07        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Z TCGA-VS-A957 
       32.15        46.03        11.51        49.55        23.24        42.08 
TCGA-VS-A959 
       39.35 

$`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-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
      101.82       134.33       147.35        17.19        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YT TCGA-C5-A8ZZ 
        9.34        13.61        50.99         8.35         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM 
        4.47         1.12        58.88        44.94        40.04        58.88 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
        2.66       117.99        22.98        16.18        17.52         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-A44S TCGA-EA-A4BA TCGA-EA-A556 
        1.18        14.50         1.35        12.66        12.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2H1 
        1.48        13.91        15.02        13.58        45.96        26.27 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RB TCGA-EK-A2RC 
        6.64         0.43         0.59         1.45         0.07         4.04 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK 
        0.36         1.18        23.70         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K 
        0.03         7.92         6.94        14.70         4.73         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX 
       23.84         0.92         2.17         0.66         1.02         1.48 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41         7.13        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      147.39        96.95        78.71        26.56        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        21.44        15.58        10.06         5.13 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW 
        6.71        21.11       195.85        30.31         7.99         0.89 
TCGA-LP-A5U2 TCGA-MU-A8JM TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        0.30         5.42         5.49        15.58        15.95        16.14 
TCGA-Q1-A73O TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PI TCGA-VS-A8EC 
       14.07         6.25        10.39         3.88        61.28        34.52 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 
       23.28        39.78        31.27        16.64         4.73        44.88 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        43.82        38.96        18.05 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            182.93             195.85 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            17.560             14.975 
[1] "0.0 - 182.9 (17.6)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1.4"
D62V2, continuous
                    vv
clus                 T1 T2 T3+T4
  11Q LOSS MUTATED   44 18     5
  11Q LOSS WILD-TYPE 77 32     6
D62V3, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                  44                 77
  T2                  18                 32
  T3+T4                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   40 15
  11Q LOSS WILD-TYPE 71 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     40   15
  11Q LOSS WILD-TYPE   71   32
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               40                 71
  1               15                 32
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED   35  3 35
  11Q LOSS WILD-TYPE 56  5 58
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               35                 56
  M1                3                  5
  MX               35                 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
  11Q LOSS MUTATED               0                               84
  11Q LOSS WILD-TYPE             5                              113
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11Q LOSS MUTATED                                     6
  11Q LOSS WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11Q LOSS MUTATED                                           1
  11Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11Q LOSS MUTATED                                              1
  11Q LOSS WILD-TYPE                                            5
D62V6, multiclass
                                               clus
vv                                              11Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              11Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             113
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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    11  82
  11Q LOSS WILD-TYPE  19 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     11   82
  11Q LOSS WILD-TYPE   19  126
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                11                 19
  YES               82                126
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  2    11
  11Q LOSS WILD-TYPE                                6     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED                          10
  11Q LOSS WILD-TYPE                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           1    63
  11Q LOSS WILD-TYPE                                         0   106
D62V10, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                   11                  7
  BLACK OR AFRICAN AMERICAN                               10                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   63                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"
D62V11, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    3 57
  11Q LOSS WILD-TYPE 13 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   57
  11Q LOSS WILD-TYPE   13   92
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               57                 92
[1] 2 2
[1] FALSE
D62V12, continuous
D62V13, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   24 13
  11Q LOSS WILD-TYPE 47 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     24   13
  11Q LOSS WILD-TYPE   47   12
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  TUMOR FREE               24                 47
  WITH TUMOR               13                 12
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  11Q LOSS MUTATED       13      1       1      2       2            65       9
  11Q LOSS WILD-TYPE     10      4       0      8       5           113       5
D62V14, multiclass
               clus
vv              11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  BRAZIL                      13                 10
  CANADA                       1                  4
  NIGERIA                      1                  0
  RUSSIA                       2                  8
  UKRAINE                      2                  5
  UNITED STATES               65                113
  VIETNAM                      9                  5
[1] 7 2
[1] 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    5 40 40  0  6
  11Q LOSS WILD-TYPE 12 66 57  1  8
D62V15, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  G1                5                 12
  G2               40                 66
  G3               40                 57
  G4                0                  1
  GX                6                  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"
D62V16, continuous
D62V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11Q LOSS MUTATED                                            13
  11Q LOSS WILD-TYPE                                          18
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11Q LOSS MUTATED               20                  44
  11Q LOSS WILD-TYPE             32                  68
D62V18, multiclass
                                                 clus
vv                                                11Q LOSS MUTATED
  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                                           44
                                                 clus
vv                                                11Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  32
  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"
D62V19, continuous
D62V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  11Q LOSS MUTATED             8       30             3        5
  11Q LOSS WILD-TYPE          11       45             9        7
D62V21, multiclass
               clus
vv              11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COMBINATION                  8                 11
  EXTERNAL                    30                 45
  EXTERNAL BEAM                3                  9
  INTERNAL                     5                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V22, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    9  1
  11Q LOSS WILD-TYPE 16  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9    1
  11Q LOSS WILD-TYPE   16    2
                         clus
vv                        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  11Q LOSS MUTATED                    1                0                  11
  11Q LOSS WILD-TYPE                  1                2                  17
                    vv
clus                 REGIONAL SITE
  11Q LOSS MUTATED               9
  11Q LOSS WILD-TYPE             7
D62V23, multiclass
                     clus
vv                    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 1                  1
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD               11                 17
  REGIONAL SITE                      9                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V24, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   14  2
  11Q LOSS WILD-TYPE 20  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     14    2
  11Q LOSS WILD-TYPE   20    1
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CGY               14                 20
  GY                 2                  1
[1] 2 2
[1] FALSE
D62V25, continuous
D62V26, continuous
D62V27, continuous
D62V28, continuous
D62V29, continuous
D62V30, 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                        10                       1
  11Q LOSS WILD-TYPE                      19                       0
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11Q LOSS MUTATED                         1
  11Q LOSS WILD-TYPE                       6
D62V31, multiclass
                                     clus
vv                                    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                           10                 19
  POSITIVE BLADDER MARGIN                            1                  0
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11Q LOSS MUTATED                                               10
  11Q LOSS WILD-TYPE                                              6
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11Q LOSS MUTATED                                                                                  36
  11Q LOSS WILD-TYPE                                                                                32
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11Q LOSS MUTATED                                                                                             29
  11Q LOSS WILD-TYPE                                                                                           76
D62V32, multiclass
                                                                                              clus
vv                                                                                             11Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          36
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               29
                                                                                              clus
vv                                                                                             11Q LOSS 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)                            32
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V33, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   21 28
  11Q LOSS WILD-TYPE 47 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     21   28
  11Q LOSS WILD-TYPE   47   42
         clus
vv        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ABSENT                21                 47
  PRESENT               28                 42
[1] 2 2
[1] FALSE
D62V34, continuous
D62V35, continuous
D62V36, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   18 33
  11Q LOSS WILD-TYPE 25 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     18   33
  11Q LOSS WILD-TYPE   25   61
                                          clus
vv                                         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   18                 25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               33                 61
[1] 2 2
[1] FALSE
D62V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11Q LOSS MUTATED              2          16         24
  11Q LOSS WILD-TYPE            8          33         33
D62V38, multiclass
              clus
vv             11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                16                 33
  NEVER USED                 24                 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"
D62V39, continuous
D62V40, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   30  8
  11Q LOSS WILD-TYPE 59  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     30    8
  11Q LOSS WILD-TYPE   59    8
         clus
vv        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ABSENT                30                 59
  PRESENT                8                  8
[1] 2 2
[1] FALSE
D62V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  11Q LOSS MUTATED     1    1  11   26    5  2   1    2    3  10  0   4  1   0
  11Q LOSS WILD-TYPE   0    0  19   39   19  2   7    5    6  12  1   4  1   1
                    vv
clus                 TX
  11Q LOSS MUTATED    8
  11Q LOSS WILD-TYPE  6
D62V42, multiclass
      clus
vv     11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1A                 1                  0
  T1A1                1                  0
  T1B                11                 19
  T1B1               26                 39
  T1B2                5                 19
  T2                  2                  2
  T2A                 1                  7
  T2A1                2                  5
  T2A2                3                  6
  T2B                10                 12
  T3                  0                  1
  T3B                 4                  4
  T4                  1                  1
  TIS                 0                  1
  TX                  8                  6
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  11Q LOSS MUTATED         3        1         1         1       14        27
  11Q LOSS WILD-TYPE       1        1         0         0       17        42
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  11Q LOSS MUTATED           8        1         0          2          3
  11Q LOSS WILD-TYPE        24        2         6          3          4
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  11Q LOSS MUTATED          12         0         14         2         1
  11Q LOSS WILD-TYPE        15         1         20         1         6
D62V44, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   3                  1
  STAGE IA                  1                  1
  STAGE IA1                 1                  0
  STAGE IA2                 1                  0
  STAGE IB                 14                 17
  STAGE IB1                27                 42
  STAGE IB2                 8                 24
  STAGE II                  1                  2
  STAGE IIA                 0                  6
  STAGE IIA1                2                  3
  STAGE IIA2                3                  4
  STAGE IIB                12                 15
  STAGE III                 0                  1
  STAGE IIIB               14                 20
  STAGE IVA                 2                  1
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    22   6
  12P LOSS WILD-TYPE 161  44
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                28                205 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 44 
$`12P LOSS MUTATED`
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A2LV 
      177.04       173.29        30.21        35.01        40.93        73.45 
TCGA-C5-A2M1 TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-DG-A2KJ TCGA-DS-A0VK TCGA-DS-A0VL 
       38.43        60.69         2.73        58.88        36.76         2.66 
TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2PM TCGA-FU-A2QG 
       12.36         1.35         1.81         1.51         0.59         0.92 
TCGA-FU-A40J TCGA-HG-A9SC TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JX-A3PZ TCGA-LP-A4AX 
        1.35         7.13        78.71        26.56        21.11         0.07 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-VS-A8QF TCGA-VS-A94Z 
       13.35         3.39        49.55        23.24 

$`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-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91         3.58        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35       100.14         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       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34        13.61        50.99        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        50.76        44.94        40.04        87.75        58.88 
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        17.52 
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-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A44S 
       13.05         1.18        14.50         1.35        14.50        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        15.02 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       14.99        14.96        13.58        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       45.96        26.27         6.64         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       19.79         6.12         4.73         1.22        23.84         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-GH-A9DA TCGA-HG-A2PA 
        3.52         1.32         1.97         1.12         9.01        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
       66.81       117.40        96.95        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        5.13         6.71       195.85        30.31         7.99        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.89         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
        5.42        29.72         0.07         4.34         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        61.28        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       20.22        14.07        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       23.28        11.51        39.78        31.27        16.64         4.73 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       44.88        42.58        42.08        43.82        39.35        38.96 
TCGA-WL-A834 
       18.05 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.07               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            177.04             195.85 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            22.175             15.580 
[1] "0.1 - 177.0 (22.2)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                  T1  T2 T3+T4
  12P LOSS MUTATED    16   5     1
  12P LOSS WILD-TYPE 105  45    10
D63V3, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                  16                105
  T2                   5                 45
  T3+T4                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   14  7
  12P LOSS WILD-TYPE 97 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     14    7
  12P LOSS WILD-TYPE   97   40
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               14                 97
  1                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12P LOSS MUTATED   13  0 11
  12P LOSS WILD-TYPE 78  8 82
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               13                 78
  M1                0                  8
  MX               11                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED               1                               24
  12P LOSS WILD-TYPE             4                              173
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12P LOSS MUTATED                                               0
  12P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12P LOSS MUTATED                                     3
  12P LOSS WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12P LOSS MUTATED                                           0
  12P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12P LOSS MUTATED                                              1
  12P LOSS WILD-TYPE                                            5
D63V6, multiclass
                                               clus
vv                                              12P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            24
  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                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             173
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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  25
  12P LOSS WILD-TYPE  26 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4   25
  12P LOSS WILD-TYPE   26  183
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 4                 26
  YES               25                183
[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                                8    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED                           4
  12P LOSS WILD-TYPE                        20
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    23
  12P LOSS WILD-TYPE                                         1   146
D63V10, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                4                 20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   23                146
[1] 5 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  20
  12P LOSS WILD-TYPE  16 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   20
  12P LOSS WILD-TYPE   16  129
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               20                129
[1] 2 2
[1] FALSE
D63V12, continuous
D63V13, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   10  3
  12P LOSS WILD-TYPE 61 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     10    3
  12P LOSS WILD-TYPE   61   22
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  TUMOR FREE               10                 61
  WITH TUMOR                3                 22
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  12P LOSS MUTATED        2      1       0      2       1            22       1
  12P LOSS WILD-TYPE     21      4       1      8       6           156      13
D63V14, multiclass
               clus
vv              12P LOSS MUTATED 12P LOSS WILD-TYPE
  BRAZIL                       2                 21
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       2                  8
  UKRAINE                      1                  6
  UNITED STATES               22                156
  VIETNAM                      1                 13
[1] 7 2
[1] 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 14 13  1  1
  12P LOSS WILD-TYPE 17 92 84  0 13
D63V15, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  G1                0                 17
  G2               14                 92
  G3               13                 84
  G4                1                  0
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V16, continuous
D63V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12P LOSS MUTATED                                             6
  12P LOSS WILD-TYPE                                          25
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12P LOSS MUTATED                3                  16
  12P LOSS WILD-TYPE             49                  96
D63V18, multiclass
                                                 clus
vv                                                12P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                           16
                                                 clus
vv                                                12P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  49
  LIFELONG NON-SMOKER                                             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"
D63V19, continuous
D63V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  12P LOSS MUTATED             2        7             3        1
  12P LOSS WILD-TYPE          17       68             9       11
D63V21, multiclass
               clus
vv              12P LOSS MUTATED 12P LOSS WILD-TYPE
  COMBINATION                  2                 17
  EXTERNAL                     7                 68
  EXTERNAL BEAM                3                  9
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V22, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    4  0
  12P LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    0
  12P LOSS WILD-TYPE   21    3
                         clus
vv                        12P LOSS MUTATED 12P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  12P LOSS MUTATED                    0                0                   2
  12P LOSS WILD-TYPE                  2                2                  26
                    vv
clus                 REGIONAL SITE
  12P LOSS MUTATED               2
  12P LOSS WILD-TYPE            14
D63V23, multiclass
                     clus
vv                    12P LOSS MUTATED 12P LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                2                 26
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V24, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    3  0
  12P LOSS WILD-TYPE 31  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE   31    3
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  CGY                3                 31
  GY                 0                  3
[1] 2 2
[1] FALSE
D63V25, continuous
D63V26, continuous
D63V27, continuous
D63V28, continuous
D63V29, continuous
D63V30, 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                         6                       0
  12P LOSS WILD-TYPE                      23                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12P LOSS MUTATED                         2
  12P LOSS WILD-TYPE                       5
D63V31, multiclass
                                     clus
vv                                    12P LOSS MUTATED 12P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            6                 23
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  12P LOSS MUTATED                                               1
  12P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12P LOSS MUTATED                                                2
  12P LOSS WILD-TYPE                                             14
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12P LOSS MUTATED                                                                                   8
  12P LOSS WILD-TYPE                                                                                60
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12P LOSS MUTATED                                                                                             15
  12P LOSS WILD-TYPE                                                                                           90
D63V32, 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)               15
                                                                                              clus
vv                                                                                             12P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V33, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    9  8
  12P LOSS WILD-TYPE 59 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      9    8
  12P LOSS WILD-TYPE   59   62
         clus
vv        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ABSENT                 9                 59
  PRESENT                8                 62
[1] 2 2
[1] FALSE
D63V34, continuous
D63V35, continuous
D63V36, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    7  9
  12P LOSS WILD-TYPE 36 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      7    9
  12P LOSS WILD-TYPE   36   85
                                          clus
vv                                         12P LOSS MUTATED 12P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    7                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                9                 85
[1] 2 2
[1] FALSE
D63V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12P LOSS MUTATED              0           9         10
  12P LOSS WILD-TYPE           10          40         47
D63V38, multiclass
              clus
vv             12P LOSS MUTATED 12P LOSS WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 9                 40
  NEVER USED                 10                 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"
D63V39, continuous
D63V40, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   15  0
  12P LOSS WILD-TYPE 74 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     15    0
  12P LOSS WILD-TYPE   74   16
         clus
vv        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ABSENT                15                 74
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D63V41, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  12P LOSS MUTATED     0    0   7    8    1  0   1    2    0   2  0   1  0   0
  12P LOSS WILD-TYPE   1    1  23   57   23  4   7    5    9  20  1   7  2   1
                    vv
clus                 TX
  12P LOSS MUTATED    3
  12P LOSS WILD-TYPE 11
D63V42, multiclass
      clus
vv     12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 7                 23
  T1B1                8                 57
  T1B2                1                 23
  T2                  0                  4
  T2A                 1                  7
  T2A1                2                  5
  T2A2                0                  9
  T2B                 2                 20
  T3                  0                  1
  T3B                 1                  7
  T4                  0                  2
  TIS                 0                  1
  TX                  3                 11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  12P LOSS MUTATED         1        0         0         1        7         8
  12P LOSS WILD-TYPE       3        2         1         0       24        61
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  12P LOSS MUTATED           1        0         0          1          0
  12P LOSS WILD-TYPE        31        3         6          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  12P LOSS MUTATED           4         0          4         0         0
  12P LOSS WILD-TYPE        23         1         30         3         7
D63V44, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  7                 24
  STAGE IB1                 8                 61
  STAGE IB2                 1                 31
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 4                 23
  STAGE III                 0                  1
  STAGE IIIB                4                 30
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     6   3
  12Q LOSS WILD-TYPE 177  47
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                224 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 47 
$`12Q LOSS MUTATED`
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 
       30.21        35.01        40.93        60.69        13.61         2.73 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-FU-A770 
        1.51         0.59         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-A1ML TCGA-C5-A1MP 
       38.99        35.61         0.46         2.43        20.91         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       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC 
      147.35        17.19        85.55        94.95         9.34        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35        75.78        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        6.12        20.91         4.47         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        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        17.52 
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        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.48         0.36        12.59        45.96        26.27         6.64 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB 
        0.43         0.59         1.45         0.13        16.08         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-EX-A8YF 
        7.92         6.94        14.70        19.79         6.12         4.73 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.32         1.97         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
        7.99        11.28         0.89         0.07         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.20        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        4.34         5.49         2.96        15.58        13.35        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        3.39        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        10.39        19.59         3.88        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       14.07        19.96        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        49.55        39.78        31.27        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       23.24        44.88        42.58        42.08        43.82        39.35 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.59               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             60.69             195.85 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            13.610             15.915 
[1] "0.6 - 60.7 (13.6)"  "0.0 - 195.8 (15.9)"
[1] "hr=" "2"  
D64V2, continuous
                    vv
clus                  T1  T2 T3+T4
  12Q LOSS MUTATED     2   2     1
  12Q LOSS WILD-TYPE 119  48    10
D64V3, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                   2                119
  T2                   2                 48
  T3+T4                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2   3
  12Q LOSS WILD-TYPE 109  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    3
  12Q LOSS WILD-TYPE  109   44
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                2                109
  1                3                 44
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12Q LOSS MUTATED    2  0  3
  12Q LOSS WILD-TYPE 89  8 90
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                2                 89
  M1                0                  8
  MX                3                 90
[1] 3 2
[1] 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                                7
  12Q LOSS WILD-TYPE             5                              190
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12Q LOSS MUTATED                                               1
  12Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12Q LOSS MUTATED                                     1
  12Q LOSS WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12Q LOSS MUTATED                                           0
  12Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12Q LOSS MUTATED                                              1
  12Q LOSS WILD-TYPE                                            5
D64V6, multiclass
                                               clus
vv                                              12Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             7
  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                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             190
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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   7
  12Q LOSS WILD-TYPE  27 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    7
  12Q LOSS WILD-TYPE   27  201
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 3                 27
  YES                7                201
[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                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED                           2
  12Q LOSS WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0     8
  12Q LOSS WILD-TYPE                                         1   161
D64V10, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 18
  BLACK OR AFRICAN AMERICAN                                2                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                161
[1] 5 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   8
  12Q LOSS WILD-TYPE  16 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    8
  12Q LOSS WILD-TYPE   16  141
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO                8                141
[1] 2 2
[1] FALSE
D64V12, continuous
D64V13, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  1
  12Q LOSS WILD-TYPE 69 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    1
  12Q LOSS WILD-TYPE   69   24
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  TUMOR FREE                2                 69
  WITH TUMOR                1                 24
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  12Q LOSS MUTATED        0      0       0      0       0            10       0
  12Q LOSS WILD-TYPE     23      5       1     10       7           168      14
D64V14, multiclass
               clus
vv              12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  BRAZIL                       0                 23
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  7
  UNITED STATES               10                168
  VIETNAM                      0                 14
[1] 7 2
[1] 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   6   0   0
  12Q LOSS WILD-TYPE  17 102  91   1  14
D64V15, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  G1                0                 17
  G2                4                102
  G3                6                 91
  G4                0                  1
  GX                0                 14
[1] 5 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                                          31
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12Q LOSS MUTATED                3                   3
  12Q LOSS WILD-TYPE             49                 109
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                     31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  49
  LIFELONG NON-SMOKER                                            109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V19, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 65 
        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-C5-A8XI         TCGA-C5-A8YQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A8YT         TCGA-C5-A8ZZ         TCGA-C5-A907 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EA-A556         TCGA-EK-A2RA         TCGA-EX-A1H5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3TX         TCGA-FU-A3WB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-GH-A9DA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-JW-AAVH         TCGA-JX-A3Q0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-RA-A741 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PG         TCGA-VS-A8EH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A8QF         TCGA-VS-A8QM         TCGA-VS-A94Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-WL-A834 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D64V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  12Q LOSS MUTATED             1        2             2        1
  12Q LOSS WILD-TYPE          18       73            10       11
D64V21, multiclass
               clus
vv              12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COMBINATION                  1                 18
  EXTERNAL                     2                 73
  EXTERNAL BEAM                2                 10
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V22, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  0
  12Q LOSS WILD-TYPE 22  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE   22    3
                         clus
vv                        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   3                 22
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  12Q LOSS MUTATED                    0                0                   1
  12Q LOSS WILD-TYPE                  2                2                  27
                    vv
clus                 REGIONAL SITE
  12Q LOSS MUTATED               1
  12Q LOSS WILD-TYPE            15
D64V23, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 46 
        TCGA-C5-A0TN         TCGA-C5-A1BF         TCGA-C5-A1BQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-C5-A7UE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-C5-A8XJ         TCGA-C5-A8XK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A8YQ         TCGA-C5-A8YT         TCGA-C5-A8ZZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A907         TCGA-DG-A2KL         TCGA-DS-A7WF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23L         TCGA-HM-A3JJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LF         TCGA-IR-A3LH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JX-A5QV         TCGA-MY-A913 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-R2-A69V         TCGA-UC-A7PG         TCGA-VS-A8EC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A8EG         TCGA-VS-A8EH         TCGA-VS-A8EI 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A8EL         TCGA-VS-A8Q8         TCGA-VS-A8Q9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A8QC         TCGA-VS-A8QF         TCGA-VS-A8QH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A94X         TCGA-VS-A94Z         TCGA-VS-A954 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A957         TCGA-VS-A958         TCGA-VS-A959 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A9U5 
"12Q LOSS WILD-TYPE" 
D64V24, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    0  0
  12Q LOSS WILD-TYPE 34  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    0
  12Q LOSS WILD-TYPE   34    3
D64V25, continuous
D64V26, continuous
D64V27, continuous
D64V28, continuous
D64V29, continuous
D64V30, 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                         3                       0
  12Q LOSS WILD-TYPE                      26                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12Q LOSS MUTATED                         0
  12Q LOSS WILD-TYPE                       7
D64V31, multiclass
                                     clus
vv                                    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            3                 26
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  12Q LOSS MUTATED                                               1
  12Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12Q LOSS MUTATED                                                0
  12Q LOSS WILD-TYPE                                             16
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12Q LOSS MUTATED                                                                                   3
  12Q LOSS WILD-TYPE                                                                                65
                    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                                                                                          102
D64V32, 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)                                                               16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V33, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  2
  12Q LOSS WILD-TYPE 65 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    2
  12Q LOSS WILD-TYPE   65   68
         clus
vv        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ABSENT                 3                 65
  PRESENT                2                 68
[1] 2 2
[1] FALSE
D64V34, continuous
D64V35, continuous
D64V36, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  1
  12Q LOSS WILD-TYPE 40 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    1
  12Q LOSS WILD-TYPE   40   93
                                          clus
vv                                         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                 93
[1] 2 2
[1] FALSE
D64V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12Q LOSS MUTATED              0           4          1
  12Q LOSS WILD-TYPE           10          45         56
D64V38, multiclass
              clus
vv             12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 4                 45
  NEVER USED                  1                 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"
D64V39, continuous
D64V40, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  0
  12Q LOSS WILD-TYPE 86 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE   86   16
         clus
vv        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ABSENT                 3                 86
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D64V41, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  12Q LOSS MUTATED     0    0   1    1    0  0   1    0    1   0  0   1  0   0
  12Q LOSS WILD-TYPE   1    1  29   64   24  4   7    7    8  22  1   7  2   1
                    vv
clus                 TX
  12Q LOSS MUTATED    0
  12Q LOSS WILD-TYPE 14
D64V42, multiclass
      clus
vv     12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 1                 29
  T1B1                1                 64
  T1B2                0                 24
  T2                  0                  4
  T2A                 1                  7
  T2A1                0                  7
  T2A2                1                  8
  T2B                 0                 22
  T3                  0                  1
  T3B                 1                  7
  T4                  0                  2
  TIS                 0                  1
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  12Q LOSS MUTATED         0        0         0         1        0         3
  12Q LOSS WILD-TYPE       4        2         1         0       31        66
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  12Q LOSS MUTATED           0        0         0          0          0
  12Q LOSS WILD-TYPE        32        3         6          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  12Q LOSS MUTATED           1         0          3         0         1
  12Q LOSS WILD-TYPE        26         1         31         3         6
D64V44, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  0                 31
  STAGE IB1                 3                 66
  STAGE IB2                 0                 32
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 1                 26
  STAGE III                 0                  1
  STAGE IIIB                3                 31
  STAGE IVA                 0                  3
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    49  13
  13Q LOSS WILD-TYPE 134  37
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                62                171 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                 37 
$`13Q LOSS MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BF TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1MH 
       49.48        57.04        18.74        82.85        31.40        38.99 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7CO 
       73.18        83.05        52.01        18.02       154.32       147.35 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-DG-A2KJ 
       85.55        94.95         9.34        75.78        99.91        58.88 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A439 
      117.99       118.65        22.98        12.36         1.18        14.50 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RD 
       12.59        26.27         0.59         1.45        16.08         0.03 
TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.36         2.24        20.35        23.84         1.45         1.58 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.97        25.41         7.13        14.93         9.44       147.39 
TCGA-JW-A5VK TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       20.48         6.71        21.11        11.28         0.89         0.07 
TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH 
        3.39        19.59        12.16        10.03        34.52        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A957 
       14.07        19.96        49.55        31.27         4.73        42.08 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY 
       20.91        40.93         3.58        44.22        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
      100.14        38.43         0.82        17.85        20.42       182.93 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH 
      101.82       134.33        15.48        20.35        17.19        60.69 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ 
       13.61         2.73        50.99        45.83         8.35        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52         6.12        20.91         4.47         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        87.75        58.88        36.76         2.66 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18        17.52         8.28         0.76         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
        1.32         0.82         0.62        13.05        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-A5ZF TCGA-EA-A6QX 
        1.48        13.91        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL 
       13.48         0.36        45.96         6.64         1.51         0.43 
TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.59         0.13         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-EX-A8YF TCGA-FU-A23K 
        6.94        14.70        19.79         6.12         4.73         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.92         2.17         0.66         1.02         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JJ 
        3.52         1.35         1.32         1.12         9.01        21.67 
TCGA-HM-A3JK TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
       20.78       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        26.56        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       21.44        15.58        10.06         5.13       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        7.99         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
        5.42        29.72         0.07         4.34         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        13.35        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD 
       15.88         5.88         6.25        10.39         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       93.99        61.28        29.03        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       23.28        11.51        39.78        16.64        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 
       42.58        43.82        39.35 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            154.32             195.85 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             20.09              14.96 
[1] "0.0 - 154.3 (20.1)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1.3"
D65V2, continuous
                    vv
clus                 T1 T2 T3+T4
  13Q LOSS MUTATED   27 15     6
  13Q LOSS WILD-TYPE 94 35     5
D65V3, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                  27                 94
  T2                  15                 35
  T3+T4                6                  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"
D65V4, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   24 16
  13Q LOSS WILD-TYPE 87 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     24   16
  13Q LOSS WILD-TYPE   87   31
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               24                 87
  1               16                 31
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   24  4 23
  13Q LOSS WILD-TYPE 67  4 70
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               24                 67
  M1                4                  4
  MX               23                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED               2                               64
  13Q LOSS WILD-TYPE             3                              133
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  13Q LOSS MUTATED                                               0
  13Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  13Q LOSS MUTATED                                     0
  13Q LOSS WILD-TYPE                                  22
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  13Q LOSS MUTATED                                           0
  13Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  13Q LOSS MUTATED                                              0
  13Q LOSS WILD-TYPE                                            6
D65V6, multiclass
                                               clus
vv                                              13Q LOSS MUTATED
  ADENOSQUAMOUS                                                2
  CERVICAL SQUAMOUS CELL CARCINOMA                            64
  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                                                  3
  CERVICAL SQUAMOUS CELL CARCINOMA                             133
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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    10  56
  13Q LOSS WILD-TYPE  20 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     10   56
  13Q LOSS WILD-TYPE   20  152
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                10                 20
  YES               56                152
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     5
  13Q LOSS WILD-TYPE                                7    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED                           7
  13Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           0    48
  13Q LOSS WILD-TYPE                                         1   121
D65V10, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    5                 13
  BLACK OR AFRICAN AMERICAN                                7                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   48                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"
D65V11, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2  41
  13Q LOSS WILD-TYPE  14 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   41
  13Q LOSS WILD-TYPE   14  108
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               41                108
[1] 2 2
[1] FALSE
D65V12, continuous
D65V13, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   18  6
  13Q LOSS WILD-TYPE 53 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     18    6
  13Q LOSS WILD-TYPE   53   19
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  TUMOR FREE               18                 53
  WITH TUMOR                6                 19
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  13Q LOSS MUTATED       10      1       0      2       0            48       5
  13Q LOSS WILD-TYPE     13      4       1      8       7           130       9
D65V14, multiclass
               clus
vv              13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  BRAZIL                      10                 13
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       2                  8
  UKRAINE                      0                  7
  UNITED STATES               48                130
  VIETNAM                      5                  9
[1] 7 2
[1] 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    3 23 34  0  5
  13Q LOSS WILD-TYPE 14 83 63  1  9
D65V15, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  G1                3                 14
  G2               23                 83
  G3               34                 63
  G4                0                  1
  GX                5                  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"
D65V16, continuous
D65V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  13Q LOSS MUTATED                                             7
  13Q LOSS WILD-TYPE                                          24
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  13Q LOSS MUTATED               18                  23
  13Q LOSS WILD-TYPE             34                  89
D65V18, multiclass
                                                 clus
vv                                                13Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                18
  LIFELONG NON-SMOKER                                           23
                                                 clus
vv                                                13Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  34
  LIFELONG NON-SMOKER                                             89
[1] 5 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
D65V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  13Q LOSS MUTATED             6       24             3        1
  13Q LOSS WILD-TYPE          13       51             9       11
D65V21, multiclass
               clus
vv              13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COMBINATION                  6                 13
  EXTERNAL                    24                 51
  EXTERNAL BEAM                3                  9
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V22, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9  0
  13Q LOSS WILD-TYPE 16  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    0
  13Q LOSS WILD-TYPE   16    3
                         clus
vv                        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  13Q LOSS MUTATED                    1                0                  10
  13Q LOSS WILD-TYPE                  1                2                  18
                    vv
clus                 REGIONAL SITE
  13Q LOSS MUTATED               5
  13Q LOSS WILD-TYPE            11
D65V23, multiclass
                     clus
vv                    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 1                  1
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD               10                 18
  REGIONAL SITE                      5                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V24, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   10  1
  13Q LOSS WILD-TYPE 24  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     10    1
  13Q LOSS WILD-TYPE   24    2
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CGY               10                 24
  GY                 1                  2
[1] 2 2
[1] FALSE
D65V25, continuous
D65V26, continuous
D65V27, continuous
D65V28, continuous
D65V29, continuous
D65V30, 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                         6                       0
  13Q LOSS WILD-TYPE                      23                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  13Q LOSS MUTATED                         2
  13Q LOSS WILD-TYPE                       5
D65V31, multiclass
                                     clus
vv                                    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            6                 23
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  13Q LOSS MUTATED                                               0
  13Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  13Q LOSS MUTATED                                                6
  13Q LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  13Q LOSS MUTATED                                                                                  17
  13Q LOSS WILD-TYPE                                                                                51
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  13Q LOSS MUTATED                                                                                             27
  13Q LOSS WILD-TYPE                                                                                           78
D65V32, multiclass
                                                                                              clus
vv                                                                                             13Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               27
                                                                                              clus
vv                                                                                             13Q 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)                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V33, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   11 23
  13Q LOSS WILD-TYPE 57 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11   23
  13Q LOSS WILD-TYPE   57   47
         clus
vv        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ABSENT                11                 57
  PRESENT               23                 47
[1] 2 2
[1] FALSE
D65V34, continuous
D65V35, continuous
D65V36, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   11 28
  13Q LOSS WILD-TYPE 32 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11   28
  13Q LOSS WILD-TYPE   32   66
                                          clus
vv                                         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   11                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               28                 66
[1] 2 2
[1] FALSE
D65V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  13Q LOSS MUTATED              3          12         11
  13Q LOSS WILD-TYPE            7          37         46
D65V38, multiclass
              clus
vv             13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CURRENT USER                3                  7
  FORMER USER                12                 37
  NEVER USED                 11                 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"
D65V39, continuous
D65V40, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   14  7
  13Q LOSS WILD-TYPE 75  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     14    7
  13Q LOSS WILD-TYPE   75    9
         clus
vv        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ABSENT                14                 75
  PRESENT                7                  9
[1] 2 2
[1] FALSE
D65V41, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1ML         TCGA-C5-A1MN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  13Q LOSS MUTATED     0    0   8   12    7  3   1    2    2   7  0   6  0   0
  13Q LOSS WILD-TYPE   1    1  22   53   17  1   7    5    7  15  1   2  2   1
                    vv
clus                 TX
  13Q LOSS MUTATED    4
  13Q LOSS WILD-TYPE 10
D65V42, multiclass
      clus
vv     13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 8                 22
  T1B1               12                 53
  T1B2                7                 17
  T2                  3                  1
  T2A                 1                  7
  T2A1                2                  5
  T2A2                2                  7
  T2B                 7                 15
  T3                  0                  1
  T3B                 6                  2
  T4                  0                  2
  TIS                 0                  1
  TX                  4                 10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  13Q LOSS MUTATED         1        1         0         1       14        10
  13Q LOSS WILD-TYPE       3        1         1         0       17        59
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  13Q LOSS MUTATED           6        0         1          2          1
  13Q LOSS WILD-TYPE        26        3         5          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  13Q LOSS MUTATED          10         0         15         0         2
  13Q LOSS WILD-TYPE        17         1         19         3         5
D65V44, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  1                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                 14                 17
  STAGE IB1                10                 59
  STAGE IB2                 6                 26
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                10                 17
  STAGE III                 0                  1
  STAGE IIIB               15                 19
  STAGE IVA                 0                  3
  STAGE IVB                 2                  5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    22   5
  14Q LOSS WILD-TYPE 161  45
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                27                206 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 5                 45 
$`14Q LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE 
       23.67        57.73         0.46        83.05        38.43        18.02 
TCGA-C5-A7CM TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KJ TCGA-EA-A3Y4 TCGA-EA-A411 
       20.35        23.51        27.52        58.88        14.50         1.35 
TCGA-EA-A43B TCGA-EA-A78R TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RM 
        1.81        13.48         1.51         0.59         1.18         2.24 
TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3TX TCGA-LP-A4AU TCGA-LP-A7HU TCGA-Q1-A5R2 
        4.73        23.84         1.48        11.28         0.20        13.35 
TCGA-UC-A7PG TCGA-VS-A8QH TCGA-VS-A959 
       12.16        39.78        39.35 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       38.99        35.61         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 
       44.22        73.18        73.45        78.35       100.14         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       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       94.95         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
        8.35        75.78        99.91         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        50.76        44.94        40.04        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        17.52         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-A410 
        1.32         0.82         0.62        13.05         1.18         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-A97N 
       13.91        15.02        14.99        14.96        13.58         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 
       12.59        45.96        26.27         6.64         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         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        19.79 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
        1.97         1.12         9.01        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y 
        7.99         0.89         0.07         0.30         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
        0.03         5.42        29.72         0.07         4.34         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        15.58        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
        3.88        11.67        93.99        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       29.03        20.22        14.07        19.96        53.52        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X 
       46.03        23.28        11.51        49.55        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.20               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             83.05             195.85 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            13.480             16.015 
[1] "0.2 - 83.0 (13.5)"  "0.0 - 195.8 (16.0)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                  T1  T2 T3+T4
  14Q LOSS MUTATED    13   6     1
  14Q LOSS WILD-TYPE 108  44    10
D66V3, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                  13                108
  T2                   6                 44
  T3+T4                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V4, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   14  4
  14Q LOSS WILD-TYPE 97 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     14    4
  14Q LOSS WILD-TYPE   97   43
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               14                 97
  1                4                 43
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED   13  0  9
  14Q LOSS WILD-TYPE 78  8 84
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               13                 78
  M1                0                  8
  MX                9                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED               0                               22
  14Q LOSS WILD-TYPE             5                              175
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  14Q LOSS MUTATED                                               1
  14Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  14Q LOSS MUTATED                                     4
  14Q LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  14Q LOSS MUTATED                                           0
  14Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  14Q LOSS MUTATED                                              1
  14Q LOSS WILD-TYPE                                            5
D66V6, multiclass
                                               clus
vv                                              14Q 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                 1
                                               clus
vv                                              14Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             175
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   5
[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  27
  14Q LOSS WILD-TYPE  29 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   27
  14Q LOSS WILD-TYPE   29  181
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 1                 29
  YES               27                181
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     3
  14Q LOSS WILD-TYPE                                8    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED                           1
  14Q LOSS WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0    21
  14Q LOSS WILD-TYPE                                         1   148
D66V10, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                1                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   21                148
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  17
  14Q LOSS WILD-TYPE  15 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   17
  14Q LOSS WILD-TYPE   15  132
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               17                132
[1] 2 2
[1] FALSE
D66V12, continuous
D66V13, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   12  0
  14Q LOSS WILD-TYPE 59 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12    0
  14Q LOSS WILD-TYPE   59   25
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  TUMOR FREE               12                 59
  WITH TUMOR                0                 25
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  14Q LOSS MUTATED        2      1       0      1       2            19       3
  14Q LOSS WILD-TYPE     21      4       1      9       5           159      11
D66V14, multiclass
               clus
vv              14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  BRAZIL                       2                 21
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      2                  5
  UNITED STATES               19                159
  VIETNAM                      3                 11
[1] 7 2
[1] 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    2  9 17  0  0
  14Q LOSS WILD-TYPE 15 97 80  1 14
D66V15, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  G1                2                 15
  G2                9                 97
  G3               17                 80
  G4                0                  1
  GX                0                 14
[1] 5 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
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  14Q LOSS MUTATED                                             3
  14Q LOSS WILD-TYPE                                          28
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  14Q LOSS MUTATED                3                  15
  14Q LOSS WILD-TYPE             49                  97
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                                                 3
  LIFELONG NON-SMOKER                                           15
                                                 clus
vv                                                14Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  49
  LIFELONG NON-SMOKER                                             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"
D66V19, continuous
D66V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  14Q LOSS MUTATED             1       12             0        0
  14Q LOSS WILD-TYPE          18       63            12       12
D66V21, multiclass
               clus
vv              14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COMBINATION                  1                 18
  EXTERNAL                    12                 63
  EXTERNAL BEAM                0                 12
  INTERNAL                     0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V22, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    1  0
  14Q LOSS WILD-TYPE 24  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1    0
  14Q LOSS WILD-TYPE   24    3
                         clus
vv                        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   1                 24
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  14Q LOSS MUTATED                    0                0                   5
  14Q LOSS WILD-TYPE                  2                2                  23
                    vv
clus                 REGIONAL SITE
  14Q LOSS MUTATED               1
  14Q LOSS WILD-TYPE            15
D66V23, multiclass
                     clus
vv                    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                5                 23
  REGIONAL SITE                      1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V24, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    6  0
  14Q LOSS WILD-TYPE 28  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6    0
  14Q LOSS WILD-TYPE   28    3
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CGY                6                 28
  GY                 0                  3
[1] 2 2
[1] FALSE
D66V25, continuous
D66V26, continuous
D66V27, continuous
D66V28, continuous
D66V29, continuous
D66V30, 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                         4                       0
  14Q LOSS WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  14Q LOSS MUTATED                         1
  14Q LOSS WILD-TYPE                       6
D66V31, multiclass
                                     clus
vv                                    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            4                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  14Q LOSS MUTATED                                               0
  14Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  14Q LOSS MUTATED                                                1
  14Q LOSS WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  14Q LOSS MUTATED                                                                                  12
  14Q LOSS WILD-TYPE                                                                                56
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  14Q LOSS MUTATED                                                                                              7
  14Q LOSS WILD-TYPE                                                                                           98
D66V32, multiclass
                                                                                              clus
vv                                                                                             14Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                7
                                                                                              clus
vv                                                                                             14Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V33, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    7  8
  14Q LOSS WILD-TYPE 61 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      7    8
  14Q LOSS WILD-TYPE   61   62
         clus
vv        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ABSENT                 7                 61
  PRESENT                8                 62
[1] 2 2
[1] FALSE
D66V34, continuous
D66V35, continuous
D66V36, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    4 12
  14Q LOSS WILD-TYPE 39 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4   12
  14Q LOSS WILD-TYPE   39   82
                                          clus
vv                                         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               12                 82
[1] 2 2
[1] FALSE
D66V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  14Q LOSS MUTATED              0           5          3
  14Q LOSS WILD-TYPE           10          44         54
D66V38, multiclass
              clus
vv             14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CURRENT USER                0                 10
  FORMER USER                 5                 44
  NEVER USED                  3                 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"
D66V39, continuous
D66V40, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    9  2
  14Q LOSS WILD-TYPE 80 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      9    2
  14Q LOSS WILD-TYPE   80   14
         clus
vv        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ABSENT                 9                 80
  PRESENT                2                 14
[1] 2 2
[1] FALSE
D66V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  14Q LOSS MUTATED     0    0   3    7    3  3   0    2    0   1  0   1  0   0
  14Q LOSS WILD-TYPE   1    1  27   58   21  1   8    5    9  21  1   7  2   1
                    vv
clus                 TX
  14Q LOSS MUTATED    2
  14Q LOSS WILD-TYPE 12
D66V42, multiclass
      clus
vv     14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 3                 27
  T1B1                7                 58
  T1B2                3                 21
  T2                  3                  1
  T2A                 0                  8
  T2A1                2                  5
  T2A2                0                  9
  T2B                 1                 21
  T3                  0                  1
  T3B                 1                  7
  T4                  0                  2
  TIS                 0                  1
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  14Q LOSS MUTATED         0        0         0         0        3        12
  14Q LOSS WILD-TYPE       4        2         1         1       28        57
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  14Q LOSS MUTATED           4        1         0          1          0
  14Q LOSS WILD-TYPE        28        2         6          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  14Q LOSS MUTATED           2         0          3         0         0
  14Q LOSS WILD-TYPE        25         1         31         3         7
D66V44, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 28
  STAGE IB1                12                 57
  STAGE IB2                 4                 28
  STAGE II                  1                  2
  STAGE IIA                 0                  6
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 2                 25
  STAGE III                 0                  1
  STAGE IIIB                3                 31
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    25   8
  15Q LOSS WILD-TYPE 158  42
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                33                200 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                 42 
$`15Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1ML TCGA-C5-A2LV TCGA-C5-A7CG 
       57.04        35.01        38.99        20.91        73.45       182.93 
TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A8YQ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A7WH 
      154.32        17.19        23.51        50.76        87.75        17.52 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RN 
       14.50        14.89        12.59         0.59         1.18         0.10 
TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3LH TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-MU-A8JM 
       21.67         9.44        78.71        30.31         0.07         5.42 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-VS-A8EJ TCGA-VS-A8QH 
        5.49         2.96        15.58        13.35        19.96        39.78 
TCGA-VS-A94Z TCGA-VS-A957 TCGA-VS-A9U5 
       23.24        42.08        38.96 

$`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        20.35       147.35        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       75.78        99.91        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        58.88        44.94        40.04        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-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-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
        1.81        12.66        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       15.02        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2R7 
       45.96        26.27         6.64         1.51         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         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        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        6.12         4.73         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-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA 
       25.41         7.13        20.78        14.93       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81       117.40        96.95        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       10.06         5.13         6.71        21.11       195.85         7.99 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
       11.28         0.89         0.30         0.82         0.20        13.87 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.03        29.72         0.07         4.34        15.95         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         5.88         6.25 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       10.39        19.59         3.88        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       61.28        10.03        34.52        29.03        20.22        14.07 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       53.52        32.15        46.03        23.28        11.51        49.55 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 
       31.27        16.64         4.73        44.88        42.58        43.82 
TCGA-VS-A959 TCGA-WL-A834 
       39.35        18.05 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            182.93             195.85 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            20.910             15.005 
[1] "0.1 - 182.9 (20.9)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                  T1  T2 T3+T4
  15Q LOSS MUTATED    16   8     1
  15Q LOSS WILD-TYPE 105  42    10
D67V3, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                  16                105
  T2                   8                 42
  T3+T4                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   17  5
  15Q LOSS WILD-TYPE 94 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     17    5
  15Q LOSS WILD-TYPE   94   42
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               17                 94
  1                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED   10  3 15
  15Q LOSS WILD-TYPE 81  5 78
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               10                 81
  M1                3                  5
  MX               15                 78
[1] 3 2
[1] 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                               27
  15Q LOSS WILD-TYPE             4                              170
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  15Q LOSS MUTATED                                               0
  15Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  15Q LOSS MUTATED                                     3
  15Q LOSS WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  15Q LOSS MUTATED                                           1
  15Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  15Q LOSS MUTATED                                              2
  15Q LOSS WILD-TYPE                                            4
D67V6, multiclass
                                               clus
vv                                              15Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              15Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             170
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  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"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     4  30
  15Q LOSS WILD-TYPE  26 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4   30
  15Q LOSS WILD-TYPE   26  178
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 4                 26
  YES               30                178
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     4
  15Q LOSS WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED                           7
  15Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0    22
  15Q LOSS WILD-TYPE                                         1   147
D67V10, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                7                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   22                147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  22
  15Q LOSS WILD-TYPE  15 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   22
  15Q LOSS WILD-TYPE   15  127
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               22                127
[1] 2 2
[1] FALSE
D67V12, continuous
D67V13, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   13  5
  15Q LOSS WILD-TYPE 58 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     13    5
  15Q LOSS WILD-TYPE   58   20
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  TUMOR FREE               13                 58
  WITH TUMOR                5                 20
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  15Q LOSS MUTATED        5      1       1      1       0            24       2
  15Q LOSS WILD-TYPE     18      4       0      9       7           154      12
D67V14, multiclass
               clus
vv              15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  BRAZIL                       5                 18
  CANADA                       1                  4
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      0                  7
  UNITED STATES               24                154
  VIETNAM                      2                 12
[1] 7 2
[1] 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 10 23  1  0
  15Q LOSS WILD-TYPE 17 96 74  0 14
D67V15, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  G1                0                 17
  G2               10                 96
  G3               23                 74
  G4                1                  0
  GX                0                 14
[1] 5 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                                             4
  15Q LOSS WILD-TYPE                                          27
                    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                                                 1
  15Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  15Q LOSS MUTATED                6                  14
  15Q LOSS WILD-TYPE             46                  98
D67V18, multiclass
                                                 clus
vv                                                15Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 6
  LIFELONG NON-SMOKER                                           14
                                                 clus
vv                                                15Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  46
  LIFELONG NON-SMOKER                                             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"
D67V19, continuous
D67V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  15Q LOSS MUTATED             2       12             2        1
  15Q LOSS WILD-TYPE          17       63            10       11
D67V21, multiclass
               clus
vv              15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COMBINATION                  2                 17
  EXTERNAL                    12                 63
  EXTERNAL BEAM                2                 10
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V22, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    4  0
  15Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    0
  15Q LOSS WILD-TYPE   21    3
                         clus
vv                        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  15Q LOSS MUTATED                    0                1                   6
  15Q LOSS WILD-TYPE                  2                1                  22
                    vv
clus                 REGIONAL SITE
  15Q LOSS MUTATED               1
  15Q LOSS WILD-TYPE            15
D67V23, multiclass
                     clus
vv                    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   1                  1
  PRIMARY TUMOR FIELD                6                 22
  REGIONAL SITE                      1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V24, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    7  1
  15Q LOSS WILD-TYPE 27  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    1
  15Q LOSS WILD-TYPE   27    2
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CGY                7                 27
  GY                 1                  2
[1] 2 2
[1] FALSE
D67V25, continuous
D67V26, continuous
D67V27, continuous
D67V28, continuous
D67V29, continuous
D67V30, 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                         4                       0
  15Q LOSS WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  15Q LOSS MUTATED                         1
  15Q LOSS WILD-TYPE                       6
D67V31, multiclass
                                     clus
vv                                    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            4                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  15Q LOSS MUTATED                                               0
  15Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  15Q LOSS MUTATED                                                2
  15Q LOSS WILD-TYPE                                             14
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  15Q LOSS MUTATED                                                                                  13
  15Q LOSS WILD-TYPE                                                                                55
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  15Q LOSS MUTATED                                                                                             14
  15Q LOSS WILD-TYPE                                                                                           91
D67V32, multiclass
                                                                                              clus
vv                                                                                             15Q 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)                          13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               14
                                                                                              clus
vv                                                                                             15Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V33, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    7  7
  15Q LOSS WILD-TYPE 61 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    7
  15Q LOSS WILD-TYPE   61   63
         clus
vv        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ABSENT                 7                 61
  PRESENT                7                 63
[1] 2 2
[1] FALSE
D67V34, continuous
D67V35, continuous
D67V36, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    5 14
  15Q LOSS WILD-TYPE 38 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5   14
  15Q LOSS WILD-TYPE   38   80
                                          clus
vv                                         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    5                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               14                 80
[1] 2 2
[1] FALSE
D67V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  15Q LOSS MUTATED              1           8          7
  15Q LOSS WILD-TYPE            9          41         50
D67V38, multiclass
              clus
vv             15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 8                 41
  NEVER USED                  7                 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"
D67V39, continuous
D67V40, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    8  1
  15Q LOSS WILD-TYPE 81 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8    1
  15Q LOSS WILD-TYPE   81   15
         clus
vv        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ABSENT                 8                 81
  PRESENT                1                 15
[1] 2 2
[1] FALSE
D67V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  15Q LOSS MUTATED     0    0   4   11    1  0   1    2    0   5  0   1  0   1
  15Q LOSS WILD-TYPE   1    1  26   54   23  4   7    5    9  17  1   7  2   0
                    vv
clus                 TX
  15Q LOSS MUTATED    2
  15Q LOSS WILD-TYPE 12
D67V42, multiclass
      clus
vv     15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 4                 26
  T1B1               11                 54
  T1B2                1                 23
  T2                  0                  4
  T2A                 1                  7
  T2A1                2                  5
  T2A2                0                  9
  T2B                 5                 17
  T3                  0                  1
  T3B                 1                  7
  T4                  0                  2
  TIS                 1                  0
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  15Q LOSS MUTATED         0        0         0         1        5        12
  15Q LOSS WILD-TYPE       4        2         1         0       26        57
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  15Q LOSS MUTATED           2        0         1          2          0
  15Q LOSS WILD-TYPE        30        3         5          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  15Q LOSS MUTATED           6         0          3         0         1
  15Q LOSS WILD-TYPE        21         1         31         3         6
D67V44, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  5                 26
  STAGE IB1                12                 57
  STAGE IB2                 2                 30
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                 6                 21
  STAGE III                 0                  1
  STAGE IIIB                3                 31
  STAGE IVA                 0                  3
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    18   9
  16P LOSS WILD-TYPE 165  41
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                27                206 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                 41 
$`16P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1ML 
       23.67       173.29        35.01        57.73         0.46        20.91 
TCGA-C5-A2LT TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A8XH 
       73.18        18.02       182.93        17.19        13.61        45.83 
TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-FU-A3TX 
        1.81         1.51         0.59         1.18         2.24         1.48 
TCGA-HM-A6W2 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JX-A5QV TCGA-LP-A7HU TCGA-VS-A8EB 
        9.44        66.81        96.95         7.99         0.20        10.03 
TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-WL-A834 
       34.52        19.96        18.05 

$`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-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-A3HF 
       78.35       100.14        38.43         0.82        52.01        17.85 
TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
      147.35        85.55        60.69        94.95         9.34         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99         8.35        75.78        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        6.12        20.91         4.47         1.12        58.88        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        40.04        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        17.52 
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-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        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
        0.36        12.59        45.96        26.27         6.64         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC 
        0.59         1.45         0.13        16.08         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-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-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         6.12         4.73         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-GH-A9DA 
        3.52         1.35         1.32         1.97         1.12         9.01 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 
       25.41         7.13        21.67        20.78        14.93       147.39 
TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      137.16       117.40        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       10.06         5.13         6.71        21.11       195.85        30.31 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y 
       11.28         0.89         0.07         0.30         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
        0.03         5.42        29.72         0.07         4.34         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59         3.88        11.67        93.99        12.16        61.28 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       29.03        20.22        14.07        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       23.28        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 
       39.35        38.96 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.20               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            182.93             195.85 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             18.02              15.58 
[1] "0.2 - 182.9 (18.0)" "0.0 - 195.8 (15.6)"
[1] "hr=" "1.6"
D68V2, continuous
                    vv
clus                  T1  T2 T3+T4
  16P LOSS MUTATED    17   3     3
  16P LOSS WILD-TYPE 104  47     8
D68V3, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                  17                104
  T2                   3                 47
  T3+T4                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   17  3
  16P LOSS WILD-TYPE 94 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     17    3
  16P LOSS WILD-TYPE   94   44
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               17                 94
  1                3                 44
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED   15  3  4
  16P LOSS WILD-TYPE 76  5 89
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               15                 76
  M1                3                  5
  MX                4                 89
[1] 3 2
[1] 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                               22
  16P LOSS WILD-TYPE             4                              175
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16P LOSS MUTATED                                               1
  16P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16P LOSS MUTATED                                     5
  16P LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16P LOSS MUTATED                                           0
  16P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16P LOSS MUTATED                                              0
  16P LOSS WILD-TYPE                                            6
D68V6, multiclass
                                               clus
vv                                              16P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            22
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              16P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             175
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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     4  25
  16P LOSS WILD-TYPE  26 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   25
  16P LOSS WILD-TYPE   26  183
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 4                 26
  YES               25                183
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     2
  16P LOSS WILD-TYPE                                8    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED                           3
  16P LOSS WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           0    23
  16P LOSS WILD-TYPE                                         1   146
D68V10, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                3                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   23                146
[1] 5 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  18
  16P LOSS WILD-TYPE  16 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   18
  16P LOSS WILD-TYPE   16  131
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               18                131
[1] 2 2
[1] FALSE
D68V12, continuous
D68V13, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    7  2
  16P LOSS WILD-TYPE 64 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    2
  16P LOSS WILD-TYPE   64   23
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  TUMOR FREE                7                 64
  WITH TUMOR                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  16P LOSS MUTATED        3      0       0      0       1            23       2
  16P LOSS WILD-TYPE     20      5       1     10       6           155      12
D68V14, multiclass
               clus
vv              16P LOSS MUTATED 16P LOSS WILD-TYPE
  BRAZIL                       3                 20
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      1                  6
  UNITED STATES               23                155
  VIETNAM                      2                 12
[1] 7 2
[1] 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  8 18  0  1
  16P LOSS WILD-TYPE 16 98 79  1 13
D68V15, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  G1                1                 16
  G2                8                 98
  G3               18                 79
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V16, continuous
D68V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16P LOSS MUTATED                                             5
  16P LOSS WILD-TYPE                                          26
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16P LOSS MUTATED                4                  10
  16P LOSS WILD-TYPE             48                 102
D68V18, multiclass
                                                 clus
vv                                                16P 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                                                 4
  LIFELONG NON-SMOKER                                           10
                                                 clus
vv                                                16P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  48
  LIFELONG NON-SMOKER                                            102
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V19, continuous
D68V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  16P LOSS MUTATED             2        9             2        1
  16P LOSS WILD-TYPE          17       66            10       11
D68V21, multiclass
               clus
vv              16P LOSS MUTATED 16P LOSS WILD-TYPE
  COMBINATION                  2                 17
  EXTERNAL                     9                 66
  EXTERNAL BEAM                2                 10
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V22, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  0
  16P LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    0
  16P LOSS WILD-TYPE   21    3
                         clus
vv                        16P LOSS MUTATED 16P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  16P LOSS MUTATED                    0                0                   3
  16P LOSS WILD-TYPE                  2                2                  25
                    vv
clus                 REGIONAL SITE
  16P LOSS MUTATED               1
  16P LOSS WILD-TYPE            15
D68V23, multiclass
                     clus
vv                    16P LOSS MUTATED 16P LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                3                 25
  REGIONAL SITE                      1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V24, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3  0
  16P LOSS WILD-TYPE 31  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    0
  16P LOSS WILD-TYPE   31    3
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  CGY                3                 31
  GY                 0                  3
[1] 2 2
[1] FALSE
D68V25, continuous
D68V26, continuous
D68V27, continuous
D68V28, continuous
D68V29, continuous
D68V30, 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                         7                       0
  16P LOSS WILD-TYPE                      22                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16P LOSS MUTATED                         0
  16P LOSS WILD-TYPE                       7
D68V31, multiclass
                                     clus
vv                                    16P LOSS MUTATED 16P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            7                 22
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  16P LOSS MUTATED                                               0
  16P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  16P LOSS MUTATED                                                1
  16P LOSS WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16P LOSS MUTATED                                                                                   9
  16P LOSS WILD-TYPE                                                                                59
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16P LOSS MUTATED                                                                                              9
  16P LOSS WILD-TYPE                                                                                           96
D68V32, multiclass
                                                                                              clus
vv                                                                                             16P 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)                           9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                9
                                                                                              clus
vv                                                                                             16P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            59
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V33, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    6  9
  16P LOSS WILD-TYPE 62 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6    9
  16P LOSS WILD-TYPE   62   61
         clus
vv        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ABSENT                 6                 62
  PRESENT                9                 61
[1] 2 2
[1] FALSE
D68V34, continuous
D68V35, continuous
D68V36, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    8  6
  16P LOSS WILD-TYPE 35 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      8    6
  16P LOSS WILD-TYPE   35   88
                                          clus
vv                                         16P LOSS MUTATED 16P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    8                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                6                 88
[1] 2 2
[1] FALSE
D68V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16P LOSS MUTATED              1           5          8
  16P LOSS WILD-TYPE            9          44         49
D68V38, multiclass
              clus
vv             16P LOSS MUTATED 16P LOSS WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 5                 44
  NEVER USED                  8                 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"
D68V39, continuous
D68V40, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    9  1
  16P LOSS WILD-TYPE 80 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      9    1
  16P LOSS WILD-TYPE   80   15
         clus
vv        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ABSENT                 9                 80
  PRESENT                1                 15
[1] 2 2
[1] FALSE
D68V41, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  16P LOSS MUTATED     0    0   5    9    3  1   1    0    0   1  0   3  0   0
  16P LOSS WILD-TYPE   1    1  25   56   21  3   7    7    9  21  1   5  2   1
                    vv
clus                 TX
  16P LOSS MUTATED    0
  16P LOSS WILD-TYPE 14
D68V42, multiclass
      clus
vv     16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 5                 25
  T1B1                9                 56
  T1B2                3                 21
  T2                  1                  3
  T2A                 1                  7
  T2A1                0                  7
  T2A2                0                  9
  T2B                 1                 21
  T3                  0                  1
  T3B                 3                  5
  T4                  0                  2
  TIS                 0                  1
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  16P LOSS MUTATED         0        0         0         0        6         9
  16P LOSS WILD-TYPE       4        2         1         1       25        60
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  16P LOSS MUTATED           4        1         0          0          0
  16P LOSS WILD-TYPE        28        2         6          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  16P LOSS MUTATED           2         0          3         0         2
  16P LOSS WILD-TYPE        25         1         31         3         5
D68V44, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 25
  STAGE IB1                 9                 60
  STAGE IB2                 4                 28
  STAGE II                  1                  2
  STAGE IIA                 0                  6
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 2                 25
  STAGE III                 0                  1
  STAGE IIIB                3                 31
  STAGE IVA                 0                  3
  STAGE IVB                 2                  5
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    25   7
  16Q LOSS WILD-TYPE 158  43
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                32                201 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                 43 
$`16Q LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1ML 
       23.67       173.29        35.01        57.73         0.46        20.91 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG 
       44.22        73.18        83.05        38.43        18.02       182.93 
TCGA-C5-A7CO TCGA-C5-A8XH TCGA-DS-A7WH TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2PM 
      147.35        45.83        17.52         1.81         1.51         0.59 
TCGA-EK-A2RJ TCGA-EX-A1H6 TCGA-EX-A8YF TCGA-FU-A3TX TCGA-FU-A770 TCGA-IR-A3LA 
        1.18         7.92         4.73         1.48         1.12       137.16 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MY-A5BF TCGA-VS-A8EC 
       66.81        96.95         7.99         0.20         4.34        34.52 
TCGA-VS-A8EJ TCGA-VS-A8Q8 
       19.96        32.15 

$`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-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ 
        2.43        40.93         3.58        73.45        78.35       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
        0.82        52.01        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48        20.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI 
       94.95         9.34        13.61         2.73        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        4.47         1.12        58.88        50.76        44.94        40.04 
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-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       22.98        16.83        16.18         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-A44S TCGA-EA-A4BA 
       14.50         1.35         1.35        14.50        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        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       26.27         6.64         0.43         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       16.08         0.07         4.04         0.03         0.36        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-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
       20.35         6.94        14.70        19.79         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        9.01        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
        9.44       147.39       117.40        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        10.06         5.13         6.71        21.11       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       30.31        11.28         0.89         0.07         0.30         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 
       13.87         0.03         5.42        29.72         0.07         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59         3.88        11.67        93.99        12.16        61.28 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 
       10.03        29.03        20.22        14.07        53.52        46.03 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X 
       23.28        11.51        49.55        39.78        31.27        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        23.24        44.88        42.58        42.08        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.20               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            182.93             195.85 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             22.29              15.02 
[1] "0.2 - 182.9 (22.3)" "0.0 - 195.8 (15.0)"
[1] "hr=" "1.4"
D69V2, continuous
                    vv
clus                  T1  T2 T3+T4
  16Q LOSS MUTATED    21   6     2
  16Q LOSS WILD-TYPE 100  44     9
D69V3, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                  21                100
  T2                   6                 44
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   23  4
  16Q LOSS WILD-TYPE 88 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     23    4
  16Q LOSS WILD-TYPE   88   43
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               23                 88
  1                4                 43
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED   17  1 11
  16Q LOSS WILD-TYPE 74  7 82
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               17                 74
  M1                1                  7
  MX               11                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED               0                               22
  16Q LOSS WILD-TYPE             5                              175
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16Q LOSS MUTATED                                               3
  16Q LOSS WILD-TYPE                                             2
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16Q LOSS MUTATED                                     9
  16Q LOSS WILD-TYPE                                  13
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16Q LOSS MUTATED                                           1
  16Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16Q LOSS MUTATED                                              0
  16Q LOSS WILD-TYPE                                            6
D69V6, multiclass
                                               clus
vv                                              16Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            22
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              16Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             175
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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     5  30
  16Q LOSS WILD-TYPE  25 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   30
  16Q LOSS WILD-TYPE   25  178
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 5                 25
  YES               30                178
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     2
  16Q LOSS WILD-TYPE                                8    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED                           1
  16Q LOSS WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           0    31
  16Q LOSS WILD-TYPE                                         1   138
D69V10, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                1                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   31                138
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  21
  16Q LOSS WILD-TYPE  15 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   21
  16Q LOSS WILD-TYPE   15  128
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               21                128
[1] 2 2
[1] FALSE
D69V12, continuous
D69V13, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   11  2
  16Q LOSS WILD-TYPE 60 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     11    2
  16Q LOSS WILD-TYPE   60   23
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  TUMOR FREE               11                 60
  WITH TUMOR                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  16Q LOSS MUTATED        3      0       0      0       1            29       2
  16Q LOSS WILD-TYPE     20      5       1     10       6           149      12
D69V14, multiclass
               clus
vv              16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  BRAZIL                       3                 20
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      1                  6
  UNITED STATES               29                149
  VIETNAM                      2                 12
[1] 7 2
[1] 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 15 15  0  0
  16Q LOSS WILD-TYPE 13 91 82  1 14
D69V15, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  G1                4                 13
  G2               15                 91
  G3               15                 82
  G4                0                  1
  GX                0                 14
[1] 5 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                                             4
  16Q LOSS WILD-TYPE                                          27
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16Q LOSS MUTATED                5                  18
  16Q LOSS WILD-TYPE             47                  94
D69V18, multiclass
                                                 clus
vv                                                16Q 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                                                 5
  LIFELONG NON-SMOKER                                           18
                                                 clus
vv                                                16Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  47
  LIFELONG NON-SMOKER                                             94
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V19, continuous
D69V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  16Q LOSS MUTATED             3        9             2        2
  16Q LOSS WILD-TYPE          16       66            10       10
D69V21, multiclass
               clus
vv              16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COMBINATION                  3                 16
  EXTERNAL                     9                 66
  EXTERNAL BEAM                2                 10
  INTERNAL                     2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V22, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    5  0
  16Q LOSS WILD-TYPE 20  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    0
  16Q LOSS WILD-TYPE   20    3
                         clus
vv                        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   5                 20
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  16Q LOSS MUTATED                    0                0                   2
  16Q LOSS WILD-TYPE                  2                2                  26
                    vv
clus                 REGIONAL SITE
  16Q LOSS MUTATED               3
  16Q LOSS WILD-TYPE            13
D69V23, multiclass
                     clus
vv                    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                2                 26
  REGIONAL SITE                      3                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V24, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    5  0
  16Q LOSS WILD-TYPE 29  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    0
  16Q LOSS WILD-TYPE   29    3
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CGY                5                 29
  GY                 0                  3
[1] 2 2
[1] FALSE
D69V25, continuous
D69V26, continuous
D69V27, continuous
D69V28, continuous
D69V29, continuous
D69V30, 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                         8                       0
  16Q LOSS WILD-TYPE                      21                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16Q LOSS MUTATED                         1
  16Q LOSS WILD-TYPE                       6
D69V31, multiclass
                                     clus
vv                                    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            8                 21
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  16Q LOSS MUTATED                                               0
  16Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  16Q LOSS MUTATED                                                1
  16Q LOSS WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16Q LOSS MUTATED                                                                                  14
  16Q LOSS WILD-TYPE                                                                                54
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16Q LOSS MUTATED                                                                                             12
  16Q LOSS WILD-TYPE                                                                                           93
D69V32, multiclass
                                                                                              clus
vv                                                                                             16Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               12
                                                                                              clus
vv                                                                                             16Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  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)                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V33, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   11 10
  16Q LOSS WILD-TYPE 57 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     11   10
  16Q LOSS WILD-TYPE   57   60
         clus
vv        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ABSENT                11                 57
  PRESENT               10                 60
[1] 2 2
[1] FALSE
D69V34, continuous
D69V35, continuous
D69V36, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    8  6
  16Q LOSS WILD-TYPE 35 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8    6
  16Q LOSS WILD-TYPE   35   88
                                          clus
vv                                         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    8                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                6                 88
[1] 2 2
[1] FALSE
D69V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16Q LOSS MUTATED              2           8          8
  16Q LOSS WILD-TYPE            8          41         49
D69V38, multiclass
              clus
vv             16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                 8                 41
  NEVER USED                  8                 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"
D69V39, continuous
D69V40, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   15  1
  16Q LOSS WILD-TYPE 74 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     15    1
  16Q LOSS WILD-TYPE   74   15
         clus
vv        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ABSENT                15                 74
  PRESENT                1                 15
[1] 2 2
[1] FALSE
D69V41, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 12 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  16Q LOSS MUTATED     0    0   5   12    4  2   0    1    2   1  0   2  0   0
  16Q LOSS WILD-TYPE   1    1  25   53   20  2   8    6    7  21  1   6  2   1
                    vv
clus                 TX
  16Q LOSS MUTATED    0
  16Q LOSS WILD-TYPE 14
D69V42, multiclass
      clus
vv     16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 5                 25
  T1B1               12                 53
  T1B2                4                 20
  T2                  2                  2
  T2A                 0                  8
  T2A1                1                  6
  T2A2                2                  7
  T2B                 1                 21
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  16Q LOSS MUTATED         0        0         0         0        5        15
  16Q LOSS WILD-TYPE       4        2         1         1       26        54
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  16Q LOSS MUTATED           6        1         1          0          1
  16Q LOSS WILD-TYPE        26        2         5          5          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  16Q LOSS MUTATED           2         0          3         0         0
  16Q LOSS WILD-TYPE        25         1         31         3         7
D69V44, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  5                 26
  STAGE IB1                15                 54
  STAGE IB2                 6                 26
  STAGE II                  1                  2
  STAGE IIA                 1                  5
  STAGE IIA1                0                  5
  STAGE IIA2                1                  6
  STAGE IIB                 2                 25
  STAGE III                 0                  1
  STAGE IIIB                3                 31
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    55  21
  17P LOSS WILD-TYPE 128  29
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                76                157 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                21                 29 
$`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-C5-A7XC 
      147.35        17.19         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DR-A0ZL 
       45.83        75.78        23.51        20.91        58.88        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A439 TCGA-EA-A43B 
       36.76         2.66       118.65        12.36        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       12.66        14.99        14.96        13.58        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD 
       45.96         1.51         1.45         0.13        16.08         0.03 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A3L1 
        1.18         2.24         0.10         0.10        20.35         6.94 
TCGA-EX-A69M TCGA-FU-A3NI TCGA-GH-A9DA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI 
        6.12         1.45         9.01        78.71        26.56        24.56 
TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A5R2 
       10.06        11.28         0.89         0.03         2.96        13.35 
TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI 
        3.39         5.88        10.39         3.88        12.16        61.28 
TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y 
       10.03        14.07        11.51        49.55        39.78         4.73 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       42.58        42.08        43.82        39.35 

$`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-A1ML 
       57.73        53.16        35.61         0.46         2.43        20.91 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 
        3.58        44.22        73.45        78.35       100.14         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       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
      101.82       134.33        20.35        85.55        60.69        94.95 
TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH 
        8.35        99.91        27.52         6.12         4.47         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ 
       50.76        44.94        40.04        58.88       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18        17.52         8.28         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-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.35         1.35        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL 
       13.91        15.02        12.59        26.27         6.64         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL 
        0.59         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        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.73         1.22        23.84         0.92         2.17         0.66 
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-HG-A9SC TCGA-HM-A3JJ 
        1.32         1.97         1.12        25.41         7.13        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      117.40        96.95        81.96        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        20.48        15.58         5.13         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
      195.85        30.31         7.99         0.07         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.20        13.87         5.42        29.72         0.07         4.34 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        5.49        15.58        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EC 
       15.88         6.25        19.59        11.67        93.99        34.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       29.03        20.22        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A9U5 
       23.28        31.27        16.64        23.24        44.88        38.96 
TCGA-WL-A834 
       18.05 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            173.29             195.85 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            14.285             16.640 
[1] "0.0 - 173.3 (14.3)" "0.0 - 195.8 (16.6)"
[1] "hr=" "1.5"
D70V2, continuous
                    vv
clus                 T1 T2 T3+T4
  17P LOSS MUTATED   36 15     4
  17P LOSS WILD-TYPE 85 35     7
D70V3, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                  36                 85
  T2                  15                 35
  T3+T4                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V4, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   28 15
  17P LOSS WILD-TYPE 83 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     28   15
  17P LOSS WILD-TYPE   83   32
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               28                 83
  1               15                 32
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   28  1 30
  17P LOSS WILD-TYPE 63  7 63
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               28                 63
  M1                1                  7
  MX               30                 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 LOSS MUTATED               1                               71
  17P LOSS WILD-TYPE             4                              126
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17P LOSS MUTATED                                               0
  17P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17P LOSS MUTATED                                     3
  17P LOSS WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17P LOSS MUTATED                                           1
  17P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17P LOSS MUTATED                                              2
  17P LOSS WILD-TYPE                                            4
D70V6, multiclass
                                               clus
vv                                              17P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            71
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              17P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             126
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  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"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    11  67
  17P LOSS WILD-TYPE  19 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     11   67
  17P LOSS WILD-TYPE   19  141
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                11                 19
  YES               67                141
[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                                6    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED                           6
  17P LOSS WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1    57
  17P LOSS WILD-TYPE                                         0   112
D70V10, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    8                 10
  BLACK OR AFRICAN AMERICAN                                6                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   57                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"
D70V11, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4 50
  17P LOSS WILD-TYPE 12 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   50
  17P LOSS WILD-TYPE   12   99
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               50                 99
[1] 2 2
[1] FALSE
D70V12, continuous
D70V13, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   22  9
  17P LOSS WILD-TYPE 49 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     22    9
  17P LOSS WILD-TYPE   49   16
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  TUMOR FREE               22                 49
  WITH TUMOR                9                 16
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  17P LOSS MUTATED       10      1       1      1       3            55       7
  17P LOSS WILD-TYPE     13      4       0      9       4           123       7
D70V14, multiclass
               clus
vv              17P LOSS MUTATED 17P LOSS WILD-TYPE
  BRAZIL                      10                 13
  CANADA                       1                  4
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      3                  4
  UNITED STATES               55                123
  VIETNAM                      7                  7
[1] 7 2
[1] 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    3 34 31  1  7
  17P LOSS WILD-TYPE 14 72 66  0  7
D70V15, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  G1                3                 14
  G2               34                 72
  G3               31                 66
  G4                1                  0
  GX                7                  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"
D70V16, continuous
D70V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17P LOSS MUTATED                                            11
  17P LOSS WILD-TYPE                                          20
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17P LOSS MUTATED               18                  31
  17P LOSS WILD-TYPE             34                  81
D70V18, multiclass
                                                 clus
vv                                                17P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                18
  LIFELONG NON-SMOKER                                           31
                                                 clus
vv                                                17P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  34
  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"
D70V19, continuous
D70V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  17P LOSS MUTATED             8       29             4        4
  17P LOSS WILD-TYPE          11       46             8        8
D70V21, multiclass
               clus
vv              17P LOSS MUTATED 17P LOSS WILD-TYPE
  COMBINATION                  8                 11
  EXTERNAL                    29                 46
  EXTERNAL BEAM                4                  8
  INTERNAL                     4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V22, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    9  1
  17P LOSS WILD-TYPE 16  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9    1
  17P LOSS WILD-TYPE   16    2
                         clus
vv                        17P LOSS MUTATED 17P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  17P LOSS MUTATED                    0                0                  10
  17P LOSS WILD-TYPE                  2                2                  18
                    vv
clus                 REGIONAL SITE
  17P LOSS MUTATED               9
  17P LOSS WILD-TYPE             7
D70V23, multiclass
                     clus
vv                    17P LOSS MUTATED 17P LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD               10                 18
  REGIONAL SITE                      9                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V24, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   13  1
  17P LOSS WILD-TYPE 21  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     13    1
  17P LOSS WILD-TYPE   21    2
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  CGY               13                 21
  GY                 1                  2
[1] 2 2
[1] FALSE
D70V25, continuous
D70V26, continuous
D70V27, continuous
D70V28, continuous
D70V29, continuous
D70V30, 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                        11                       0
  17P LOSS WILD-TYPE                      18                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17P LOSS MUTATED                         3
  17P LOSS WILD-TYPE                       4
D70V31, multiclass
                                     clus
vv                                    17P LOSS MUTATED 17P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                           11                 18
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  17P LOSS MUTATED                                               1
  17P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17P LOSS MUTATED                                                6
  17P LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17P LOSS MUTATED                                                                                  23
  17P LOSS WILD-TYPE                                                                                45
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17P LOSS MUTATED                                                                                             33
  17P LOSS WILD-TYPE                                                                                           72
D70V32, multiclass
                                                                                              clus
vv                                                                                             17P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               33
                                                                                              clus
vv                                                                                             17P 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)                            45
  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"
D70V33, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   19 20
  17P LOSS WILD-TYPE 49 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19   20
  17P LOSS WILD-TYPE   49   50
         clus
vv        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ABSENT                19                 49
  PRESENT               20                 50
[1] 2 2
[1] FALSE
D70V34, continuous
D70V35, continuous
D70V36, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   19 32
  17P LOSS WILD-TYPE 24 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19   32
  17P LOSS WILD-TYPE   24   62
                                          clus
vv                                         17P LOSS MUTATED 17P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   19                 24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               32                 62
[1] 2 2
[1] FALSE
D70V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17P LOSS MUTATED              3          12         20
  17P LOSS WILD-TYPE            7          37         37
D70V38, multiclass
              clus
vv             17P LOSS MUTATED 17P LOSS WILD-TYPE
  CURRENT USER                3                  7
  FORMER USER                12                 37
  NEVER USED                 20                 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"
D70V39, continuous
D70V40, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   27  4
  17P LOSS WILD-TYPE 62 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     27    4
  17P LOSS WILD-TYPE   62   12
         clus
vv        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ABSENT                27                 62
  PRESENT                4                 12
[1] 2 2
[1] FALSE
D70V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  17P LOSS MUTATED     0    1  10   18    7  2   1    3    2   7  0   4  0   0
  17P LOSS WILD-TYPE   1    0  20   47   17  2   7    4    7  15  1   4  2   1
                    vv
clus                 TX
  17P LOSS MUTATED    6
  17P LOSS WILD-TYPE  8
D70V42, multiclass
      clus
vv     17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                1                  0
  T1B                10                 20
  T1B1               18                 47
  T1B2                7                 17
  T2                  2                  2
  T2A                 1                  7
  T2A1                3                  4
  T2A2                2                  7
  T2B                 7                 15
  T3                  0                  1
  T3B                 4                  4
  T4                  0                  2
  TIS                 0                  1
  TX                  6                  8
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  17P LOSS MUTATED         2        1         1         1       11        20
  17P LOSS WILD-TYPE       2        1         0         0       20        49
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  17P LOSS MUTATED           9        0         1          3          1
  17P LOSS WILD-TYPE        23        3         5          2          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  17P LOSS MUTATED          12         0         12         1         1
  17P LOSS WILD-TYPE        15         1         22         2         6
D70V44, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                  1                  1
  STAGE IA1                 1                  0
  STAGE IA2                 1                  0
  STAGE IB                 11                 20
  STAGE IB1                20                 49
  STAGE IB2                 9                 23
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                3                  2
  STAGE IIA2                1                  6
  STAGE IIB                12                 15
  STAGE III                 0                  1
  STAGE IIIB               12                 22
  STAGE IVA                 1                  2
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    19  10
  17Q LOSS WILD-TYPE 164  40
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                29                204 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                10                 40 
$`17Q LOSS MUTATED`
TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A7CO TCGA-C5-A7UC 
       38.99        40.93        73.18        83.05       147.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8YQ TCGA-DG-A2KJ TCGA-DS-A0VK 
       60.69         9.34         2.73        23.51        58.88        36.76 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A43B TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2R8 
      118.65        12.36         1.81         0.36         1.51         1.45 
TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EX-A69M TCGA-GH-A9DA TCGA-JW-A5VI 
        0.03         1.18         0.10         6.12         9.01        24.56 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A954 
       12.16        61.28        11.51        39.78        42.58 

$`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-A1ML 
       57.73        53.16        35.61         0.46         2.43        20.91 
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-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 
      154.32       101.82       134.33        15.48        20.35        85.55 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95        13.61        50.99        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       99.91        27.52         6.12        20.91         4.47         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       50.76        44.94        40.04        87.75        58.88         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        17.52         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-A439 TCGA-EA-A44S 
        1.18        14.50         1.35         1.35        14.50        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        15.02 
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-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
       26.27         6.64         0.43         0.59         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
       16.08         0.07         4.04         0.36        23.70         2.24 
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-A8YF TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70        19.79         4.73         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-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12        25.41         7.13        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       195.85        30.31         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
        5.42        29.72         0.07         4.34         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        13.35        15.95         3.39        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
        3.88        11.67        93.99        10.03        34.52        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       20.22        14.07        19.96        53.52        32.15        46.03 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       23.28        49.55        31.27        16.64         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       44.88        42.08        43.82        39.35        38.96        18.05 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.03               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            147.35             195.85 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             17.19              15.73 
[1] "0.0 - 147.3 (17.2)" "0.0 - 195.8 (15.7)"
[1] "hr=" "1.5"
D71V2, continuous
                    vv
clus                  T1  T2 T3+T4
  17Q LOSS MUTATED    15   4     2
  17Q LOSS WILD-TYPE 106  46     9
D71V3, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                  15                106
  T2                   4                 46
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   12  7
  17Q LOSS WILD-TYPE 99 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     12    7
  17Q LOSS WILD-TYPE   99   40
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               12                 99
  1                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED   10  0 13
  17Q LOSS WILD-TYPE 81  8 80
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0               10                 81
  M1                0                  8
  MX               13                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED               0                               27
  17Q LOSS WILD-TYPE             5                              170
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17Q LOSS MUTATED                                     0
  17Q LOSS WILD-TYPE                                  22
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17Q LOSS MUTATED                                           1
  17Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17Q LOSS MUTATED                                              2
  17Q LOSS WILD-TYPE                                            4
D71V6, multiclass
                                               clus
vv                                              17Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              17Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             170
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           22
  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"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     5  25
  17Q LOSS WILD-TYPE  25 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5   25
  17Q LOSS WILD-TYPE   25  183
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 5                 25
  YES               25                183
[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                                6    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED                           1
  17Q LOSS WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           0    25
  17Q LOSS WILD-TYPE                                         1   144
D71V10, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    0                 18
  BLACK OR AFRICAN AMERICAN                                1                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   25                144
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  20
  17Q LOSS WILD-TYPE  15 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   20
  17Q LOSS WILD-TYPE   15  129
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               20                129
[1] 2 2
[1] FALSE
D71V12, continuous
D71V13, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    8  2
  17Q LOSS WILD-TYPE 63 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8    2
  17Q LOSS WILD-TYPE   63   23
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  TUMOR FREE                8                 63
  WITH TUMOR                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  17Q LOSS MUTATED        3      1       0      1       2            23       0
  17Q LOSS WILD-TYPE     20      4       1      9       5           155      14
D71V14, multiclass
               clus
vv              17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  BRAZIL                       3                 20
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      2                  5
  UNITED STATES               23                155
  VIETNAM                      0                 14
[1] 7 2
[1] 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    2 15 13  0  0
  17Q LOSS WILD-TYPE 15 91 84  1 14
D71V15, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  G1                2                 15
  G2               15                 91
  G3               13                 84
  G4                0                  1
  GX                0                 14
[1] 5 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
D71V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17Q LOSS MUTATED                                             2
  17Q LOSS WILD-TYPE                                          29
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17Q LOSS MUTATED                9                   9
  17Q LOSS WILD-TYPE             43                 103
D71V18, multiclass
                                                 clus
vv                                                17Q 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                                                 9
  LIFELONG NON-SMOKER                                            9
                                                 clus
vv                                                17Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  43
  LIFELONG NON-SMOKER                                            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"
D71V19, continuous
D71V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  17Q LOSS MUTATED             3       10             3        2
  17Q LOSS WILD-TYPE          16       65             9       10
D71V21, multiclass
               clus
vv              17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COMBINATION                  3                 16
  EXTERNAL                    10                 65
  EXTERNAL BEAM                3                  9
  INTERNAL                     2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V22, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  0
  17Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE   21    3
                         clus
vv                        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  17Q LOSS MUTATED                    0                0                   4
  17Q LOSS WILD-TYPE                  2                2                  24
                    vv
clus                 REGIONAL SITE
  17Q LOSS MUTATED               4
  17Q LOSS WILD-TYPE            12
D71V23, multiclass
                     clus
vv                    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                4                 24
  REGIONAL SITE                      4                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V24, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    6  0
  17Q LOSS WILD-TYPE 28  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      6    0
  17Q LOSS WILD-TYPE   28    3
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CGY                6                 28
  GY                 0                  3
[1] 2 2
[1] FALSE
D71V25, continuous
D71V26, continuous
D71V27, continuous
D71V28, continuous
D71V29, continuous
D71V30, 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                         5                       0
  17Q LOSS WILD-TYPE                      24                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17Q LOSS MUTATED                         2
  17Q LOSS WILD-TYPE                       5
D71V31, multiclass
                                     clus
vv                                    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            5                 24
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17Q LOSS MUTATED                                                1
  17Q LOSS WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17Q LOSS MUTATED                                                                                  12
  17Q LOSS WILD-TYPE                                                                                56
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17Q LOSS MUTATED                                                                                             10
  17Q LOSS WILD-TYPE                                                                                           95
D71V32, multiclass
                                                                                              clus
vv                                                                                             17Q 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)                          12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               10
                                                                                              clus
vv                                                                                             17Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V33, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    9  6
  17Q LOSS WILD-TYPE 59 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9    6
  17Q LOSS WILD-TYPE   59   64
         clus
vv        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ABSENT                 9                 59
  PRESENT                6                 64
[1] 2 2
[1] FALSE
D71V34, continuous
D71V35, continuous
D71V36, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    9 12
  17Q LOSS WILD-TYPE 34 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9   12
  17Q LOSS WILD-TYPE   34   82
                                          clus
vv                                         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               12                 82
[1] 2 2
[1] FALSE
D71V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17Q LOSS MUTATED              1           6          7
  17Q LOSS WILD-TYPE            9          43         50
D71V38, multiclass
              clus
vv             17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 6                 43
  NEVER USED                  7                 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"
D71V39, continuous
D71V40, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   10  0
  17Q LOSS WILD-TYPE 79 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    0
  17Q LOSS WILD-TYPE   79   16
         clus
vv        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ABSENT                10                 79
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D71V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  17Q LOSS MUTATED     0    0   5    5    5  1   1    0    0   2  0   2  0   0
  17Q LOSS WILD-TYPE   1    1  25   60   19  3   7    7    9  20  1   6  2   1
                    vv
clus                 TX
  17Q LOSS MUTATED    2
  17Q LOSS WILD-TYPE 12
D71V42, multiclass
      clus
vv     17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 5                 25
  T1B1                5                 60
  T1B2                5                 19
  T2                  1                  3
  T2A                 1                  7
  T2A1                0                  7
  T2A2                0                  9
  T2B                 2                 20
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  17Q LOSS MUTATED         0        0         0         1        5         9
  17Q LOSS WILD-TYPE       4        2         1         0       26        60
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  17Q LOSS MUTATED           5        0         0          0          0
  17Q LOSS WILD-TYPE        27        3         6          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  17Q LOSS MUTATED           1         0          7         1         0
  17Q LOSS WILD-TYPE        26         1         27         2         7
D71V44, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  5                 26
  STAGE IB1                 9                 60
  STAGE IB2                 5                 27
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 1                 26
  STAGE III                 0                  1
  STAGE IIIB                7                 27
  STAGE IVA                 1                  2
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    32  11
  18P LOSS WILD-TYPE 151  39
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                43                190 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                11                 39 
$`18P LOSS MUTATED`
TCGA-C5-A1BJ TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML 
      144.16        31.40        35.01        35.61         0.46        20.91 
TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A7CH 
       40.93        73.45        78.35        38.43         0.82       154.32 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DG-A2KM TCGA-DS-A0VN TCGA-EA-A1QS TCGA-EA-A1QT 
       13.61         2.73        40.04       118.65         0.76        12.36 
TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RM 
        1.81        12.59        26.27         6.64         1.51         2.24 
TCGA-EX-A1H6 TCGA-EX-A69L TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ TCGA-JW-A5VI 
        7.92        19.79         2.17         1.12        21.67        24.56 
TCGA-JW-A69B TCGA-LP-A4AX TCGA-LP-A7HU TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A73P 
       10.06         0.07         0.20        15.58        13.35        15.88 
TCGA-UC-A7PD TCGA-VS-A8EC TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A94Z 
       11.67        34.52        53.52        46.03        39.78        23.24 
TCGA-VS-A952 
       44.88 

$`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-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       67.46        46.32        30.21        57.73        53.16        38.99 
TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LZ 
        2.43         3.58        44.22        73.18        83.05       100.14 
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        20.35       147.35        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       60.69        94.95         9.34        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       75.78        99.91        23.51        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZL 
        4.47         1.12        58.88        50.76        44.94        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        17.52         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        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        0.36        45.96         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         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-EX-A8YF 
        0.03        20.35         6.94        14.70         6.12         4.73 
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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         9.01        25.41         7.13        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        20.48        15.58         5.13         6.71        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
      195.85        30.31         7.99        11.28         0.89         0.30 
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-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        4.34         5.49         2.96        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       17.56        14.07         5.88         6.25        10.39        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
        3.88        93.99        12.16        61.28        10.03        29.03 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC 
       20.22        14.07        19.96        32.15        23.28        11.51 
TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A954 TCGA-VS-A957 
       49.55        31.27        16.64         4.73        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            154.32             195.85 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             19.79              15.53 
[1] "0.1 - 154.3 (19.8)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                  T1  T2 T3+T4
  18P LOSS MUTATED    20   7     2
  18P LOSS WILD-TYPE 101  43     9
D72V3, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                  20                101
  T2                   7                 43
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V4, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   17  7
  18P LOSS WILD-TYPE 94 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     17    7
  18P LOSS WILD-TYPE   94   40
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               17                 94
  1                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED   15  0 17
  18P LOSS WILD-TYPE 76  8 76
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               15                 76
  M1                0                  8
  MX               17                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED               0                               30
  18P LOSS WILD-TYPE             5                              167
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18P LOSS MUTATED                                               1
  18P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18P LOSS MUTATED                                    10
  18P LOSS WILD-TYPE                                  12
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18P LOSS MUTATED                                           0
  18P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18P LOSS MUTATED                                              4
  18P LOSS WILD-TYPE                                            2
D72V6, multiclass
                                               clus
vv                                              18P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 4
                                               clus
vv                                              18P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             167
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  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     9  36
  18P LOSS WILD-TYPE  21 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9   36
  18P LOSS WILD-TYPE   21  172
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 9                 21
  YES               36                172
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  2     3
  18P LOSS WILD-TYPE                                6    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED                           6
  18P LOSS WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           0    33
  18P LOSS WILD-TYPE                                         1   136
D72V10, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                6                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   33                136
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  26
  18P LOSS WILD-TYPE  13 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   26
  18P LOSS WILD-TYPE   13  123
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               26                123
[1] 2 2
[1] FALSE
D72V12, continuous
D72V13, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   14  7
  18P LOSS WILD-TYPE 57 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     14    7
  18P LOSS WILD-TYPE   57   18
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  TUMOR FREE               14                 57
  WITH TUMOR                7                 18
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  18P LOSS MUTATED        6      1       0      2       1            33       2
  18P LOSS WILD-TYPE     17      4       1      8       6           145      12
D72V14, multiclass
               clus
vv              18P LOSS MUTATED 18P LOSS WILD-TYPE
  BRAZIL                       6                 17
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       2                  8
  UKRAINE                      1                  6
  UNITED STATES               33                145
  VIETNAM                      2                 12
[1] 7 2
[1] 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 25 17  0  1
  18P LOSS WILD-TYPE 15 81 80  1 13
D72V15, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  G1                2                 15
  G2               25                 81
  G3               17                 80
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V16, continuous
D72V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18P LOSS MUTATED                                             3
  18P LOSS WILD-TYPE                                          28
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18P LOSS MUTATED                9                  24
  18P LOSS WILD-TYPE             43                  88
D72V18, multiclass
                                                 clus
vv                                                18P 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                                                 9
  LIFELONG NON-SMOKER                                           24
                                                 clus
vv                                                18P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  43
  LIFELONG NON-SMOKER                                             88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V19, continuous
D72V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  18P LOSS MUTATED             6       10             3        1
  18P LOSS WILD-TYPE          13       65             9       11
D72V21, multiclass
               clus
vv              18P LOSS MUTATED 18P LOSS WILD-TYPE
  COMBINATION                  6                 13
  EXTERNAL                    10                 65
  EXTERNAL BEAM                3                  9
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V22, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    8  0
  18P LOSS WILD-TYPE 17  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8    0
  18P LOSS WILD-TYPE   17    3
                         clus
vv                        18P LOSS MUTATED 18P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   8                 17
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  18P LOSS MUTATED                    0                1                   5
  18P LOSS WILD-TYPE                  2                1                  23
                    vv
clus                 REGIONAL SITE
  18P LOSS MUTATED               1
  18P LOSS WILD-TYPE            15
D72V23, multiclass
                     clus
vv                    18P LOSS MUTATED 18P LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   1                  1
  PRIMARY TUMOR FIELD                5                 23
  REGIONAL SITE                      1                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V24, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    6  0
  18P LOSS WILD-TYPE 28  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6    0
  18P LOSS WILD-TYPE   28    3
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  CGY                6                 28
  GY                 0                  3
[1] 2 2
[1] FALSE
D72V25, continuous
D72V26, continuous
D72V27, continuous
D72V28, continuous
D72V29, continuous
D72V30, 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                         7                       0
  18P LOSS WILD-TYPE                      22                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18P LOSS MUTATED                         1
  18P LOSS WILD-TYPE                       6
D72V31, multiclass
                                     clus
vv                                    18P LOSS MUTATED 18P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            7                 22
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  18P LOSS MUTATED                                               0
  18P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18P LOSS MUTATED                                                3
  18P LOSS WILD-TYPE                                             13
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18P LOSS MUTATED                                                                                  15
  18P LOSS WILD-TYPE                                                                                53
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18P LOSS MUTATED                                                                                             20
  18P LOSS WILD-TYPE                                                                                           85
D72V32, multiclass
                                                                                              clus
vv                                                                                             18P 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                                                                                             18P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V33, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   16  7
  18P LOSS WILD-TYPE 52 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16    7
  18P LOSS WILD-TYPE   52   63
         clus
vv        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ABSENT                16                 52
  PRESENT                7                 63
[1] 2 2
[1] FALSE
D72V34, continuous
D72V35, continuous
D72V36, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    6 13
  18P LOSS WILD-TYPE 37 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6   13
  18P LOSS WILD-TYPE   37   81
                                          clus
vv                                         18P LOSS MUTATED 18P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               13                 81
[1] 2 2
[1] FALSE
D72V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18P LOSS MUTATED              2          17          9
  18P LOSS WILD-TYPE            8          32         48
D72V38, multiclass
              clus
vv             18P LOSS MUTATED 18P LOSS WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                17                 32
  NEVER USED                  9                 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"
D72V39, continuous
D72V40, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   17  0
  18P LOSS WILD-TYPE 72 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     17    0
  18P LOSS WILD-TYPE   72   16
         clus
vv        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ABSENT                17                 72
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D72V41, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 11 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MP 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-GH-A9DA         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3Q8         TCGA-MU-A51Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-MY-A913 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  18P LOSS MUTATED     0    0   5   13    2  1   1    0    1   4  0   2  0   0
  18P LOSS WILD-TYPE   1    1  25   52   22  3   7    7    8  18  1   6  2   1
                    vv
clus                 TX
  18P LOSS MUTATED    3
  18P LOSS WILD-TYPE 11
D72V42, multiclass
      clus
vv     18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 5                 25
  T1B1               13                 52
  T1B2                2                 22
  T2                  1                  3
  T2A                 1                  7
  T2A1                0                  7
  T2A2                1                  8
  T2B                 4                 18
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  3                 11
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  18P LOSS MUTATED         0        0         0         0        5        20
  18P LOSS WILD-TYPE       4        2         1         1       26        49
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  18P LOSS MUTATED           4        1         1          0          0
  18P LOSS WILD-TYPE        28        2         5          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  18P LOSS MUTATED           7         0          4         0         1
  18P LOSS WILD-TYPE        20         1         30         3         6
D72V44, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  5                 26
  STAGE IB1                20                 49
  STAGE IB2                 4                 28
  STAGE II                  1                  2
  STAGE IIA                 1                  5
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 7                 20
  STAGE III                 0                  1
  STAGE IIIB                4                 30
  STAGE IVA                 0                  3
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    40  17
  18Q LOSS WILD-TYPE 143  33
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                57                176 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                17                 33 
$`18Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML 
       31.40        35.01        57.73        35.61         0.46        20.91 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A7CH TCGA-C5-A7UC 
       40.93        78.35        38.43         0.82       154.32        17.19 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VN 
       13.61         2.73        99.91        40.04        87.75       118.65 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 
        0.76        12.36         1.81        14.89        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RM TCGA-EX-A1H6 
       26.27         6.64         1.51         0.59         2.24         7.92 
TCGA-EX-A3L1 TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LB 
        6.94         2.17         1.12        21.67       137.16        66.81 
TCGA-IR-A3LH TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX 
       78.71        24.56        10.06        21.11         0.89         0.07 
TCGA-LP-A7HU TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73P TCGA-RA-A741 
        0.20        15.58        13.35         3.39        15.88         3.88 
TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 
       11.67        10.03        34.52        19.96        53.52        46.03 
TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A959 
       39.78        44.88        39.35 

$`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        20.35       147.35        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       60.69        94.95         9.34        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       75.78        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        58.88        50.76        44.94        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99        22.98        16.83        16.18        17.52 
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-A411 TCGA-EA-A439 TCGA-EA-A44S 
        1.18        14.50         1.35         1.35        14.50        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        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2PL TCGA-EK-A2R7 
       14.96        13.58        13.48         0.36         0.43         0.59 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        1.45         0.13        16.08         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        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
        4.73         1.22        23.84         0.92         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
        1.32         1.97         9.01        25.41         7.13        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
       14.93         9.44       147.39       117.40        96.95        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        27.42         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       15.58         5.13         6.71       195.85        30.31         7.99 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       11.28         0.30         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 
       29.72         0.07         4.34         5.49         2.96        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        17.56        14.07         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH 
       19.59        93.99        12.16        61.28        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       14.07        32.15        23.28        11.51        49.55        31.27 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       16.64         4.73        23.24        42.58        42.08        43.82 
TCGA-VS-A9U5 TCGA-WL-A834 
       38.96        18.05 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            154.32             195.85 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             17.19              15.53 
[1] "0.1 - 154.3 (17.2)" "0.0 - 195.8 (15.5)"
[1] "hr=" "1.5"
D73V2, continuous
                    vv
clus                 T1 T2 T3+T4
  18Q LOSS MUTATED   26 10     3
  18Q LOSS WILD-TYPE 95 40     8
D73V3, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                  26                 95
  T2                  10                 40
  T3+T4                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   26  6
  18Q LOSS WILD-TYPE 85 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     26    6
  18Q LOSS WILD-TYPE   85   41
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               26                 85
  1                6                 41
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   24  2 17
  18Q LOSS WILD-TYPE 67  6 76
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               24                 67
  M1                2                  6
  MX               17                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED               0                               40
  18Q LOSS WILD-TYPE             5                              157
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18Q LOSS MUTATED                                               1
  18Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18Q LOSS MUTATED                                    12
  18Q LOSS WILD-TYPE                                  10
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18Q LOSS MUTATED                                           2
  18Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18Q LOSS MUTATED                                              4
  18Q LOSS WILD-TYPE                                            2
D73V6, multiclass
                                               clus
vv                                              18Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            40
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 4
                                               clus
vv                                              18Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             157
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           10
  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"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     9  50
  18Q LOSS WILD-TYPE  21 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9   50
  18Q LOSS WILD-TYPE   21  158
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 9                 21
  YES               50                158
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  2     4
  18Q LOSS WILD-TYPE                                6    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED                           7
  18Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           0    44
  18Q LOSS WILD-TYPE                                         1   125
D73V10, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                7                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   44                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"
D73V11, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3  32
  18Q LOSS WILD-TYPE  13 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   32
  18Q LOSS WILD-TYPE   13  117
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               32                117
[1] 2 2
[1] FALSE
D73V12, continuous
D73V13, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   17  8
  18Q LOSS WILD-TYPE 54 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     17    8
  18Q LOSS WILD-TYPE   54   17
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  TUMOR FREE               17                 54
  WITH TUMOR                8                 17
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  18Q LOSS MUTATED        8      1       0      3       1            43       3
  18Q LOSS WILD-TYPE     15      4       1      7       6           135      11
D73V14, multiclass
               clus
vv              18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  BRAZIL                       8                 15
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       3                  7
  UKRAINE                      1                  6
  UNITED STATES               43                135
  VIETNAM                      3                 11
[1] 7 2
[1] 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 24 26  1  4
  18Q LOSS WILD-TYPE 13 82 71  0 10
D73V15, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  G1                4                 13
  G2               24                 82
  G3               26                 71
  G4                1                  0
  GX                4                 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"
D73V16, continuous
D73V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18Q LOSS MUTATED                                             4
  18Q LOSS WILD-TYPE                                          27
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18Q LOSS MUTATED               10                  31
  18Q LOSS WILD-TYPE             42                  81
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                                                10
  LIFELONG NON-SMOKER                                           31
                                                 clus
vv                                                18Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  42
  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"
D73V19, continuous
D73V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  18Q LOSS MUTATED             5       18             4        1
  18Q LOSS WILD-TYPE          14       57             8       11
D73V21, multiclass
               clus
vv              18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COMBINATION                  5                 14
  EXTERNAL                    18                 57
  EXTERNAL BEAM                4                  8
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V22, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    7  1
  18Q LOSS WILD-TYPE 18  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7    1
  18Q LOSS WILD-TYPE   18    2
                         clus
vv                        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   7                 18
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  18Q LOSS MUTATED                    0                1                   7
  18Q LOSS WILD-TYPE                  2                1                  21
                    vv
clus                 REGIONAL SITE
  18Q LOSS MUTATED               2
  18Q LOSS WILD-TYPE            14
D73V23, multiclass
                     clus
vv                    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   1                  1
  PRIMARY TUMOR FIELD                7                 21
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V24, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    8  0
  18Q LOSS WILD-TYPE 26  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      8    0
  18Q LOSS WILD-TYPE   26    3
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CGY                8                 26
  GY                 0                  3
[1] 2 2
[1] FALSE
D73V25, continuous
D73V26, continuous
D73V27, continuous
D73V28, continuous
D73V29, continuous
D73V30, 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                         8                       0
  18Q LOSS WILD-TYPE                      21                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18Q LOSS MUTATED                         2
  18Q LOSS WILD-TYPE                       5
D73V31, multiclass
                                     clus
vv                                    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            8                 21
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  18Q LOSS MUTATED                                               0
  18Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18Q LOSS MUTATED                                                4
  18Q LOSS WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18Q LOSS MUTATED                                                                                  22
  18Q LOSS WILD-TYPE                                                                                46
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18Q LOSS MUTATED                                                                                             24
  18Q LOSS WILD-TYPE                                                                                           81
D73V32, multiclass
                                                                                              clus
vv                                                                                             18Q 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)                          22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               24
                                                                                              clus
vv                                                                                             18Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V33, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   19 10
  18Q LOSS WILD-TYPE 49 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     19   10
  18Q LOSS WILD-TYPE   49   60
         clus
vv        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ABSENT                19                 49
  PRESENT               10                 60
[1] 2 2
[1] FALSE
D73V34, continuous
D73V35, continuous
D73V36, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    9 17
  18Q LOSS WILD-TYPE 34 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9   17
  18Q LOSS WILD-TYPE   34   77
                                          clus
vv                                         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               17                 77
[1] 2 2
[1] FALSE
D73V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18Q LOSS MUTATED              3          19         13
  18Q LOSS WILD-TYPE            7          30         44
D73V38, multiclass
              clus
vv             18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CURRENT USER                3                  7
  FORMER USER                19                 30
  NEVER USED                 13                 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"
D73V39, continuous
D73V40, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   24  0
  18Q LOSS WILD-TYPE 65 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     24    0
  18Q LOSS WILD-TYPE   65   16
         clus
vv        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ABSENT                24                 65
  PRESENT                0                 16
[1] 2 2
[1] FALSE
D73V41, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 11 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MP 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-GH-A9DA         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3Q8         TCGA-MU-A51Y 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-MY-A913 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  18Q LOSS MUTATED     0    0   7   17    2  1   1    2    1   5  0   3  0   0
  18Q LOSS WILD-TYPE   1    1  23   48   22  3   7    5    8  17  1   5  2   1
                    vv
clus                 TX
  18Q LOSS MUTATED    4
  18Q LOSS WILD-TYPE 10
D73V42, multiclass
      clus
vv     18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 7                 23
  T1B1               17                 48
  T1B2                2                 22
  T2                  1                  3
  T2A                 1                  7
  T2A1                2                  5
  T2A2                1                  8
  T2B                 5                 17
  T3                  0                  1
  T3B                 3                  5
  T4                  0                  2
  TIS                 0                  1
  TX                  4                 10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  18Q LOSS MUTATED         1        1         0         0        7        23
  18Q LOSS WILD-TYPE       3        1         1         1       24        46
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  18Q LOSS MUTATED           4        1         1          2          0
  18Q LOSS WILD-TYPE        28        2         5          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  18Q LOSS MUTATED          10         0          5         0         1
  18Q LOSS WILD-TYPE        17         1         29         3         6
D73V44, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  1                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  7                 24
  STAGE IB1                23                 46
  STAGE IB2                 4                 28
  STAGE II                  1                  2
  STAGE IIA                 1                  5
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                10                 17
  STAGE III                 0                  1
  STAGE IIIB                5                 29
  STAGE IVA                 0                  3
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    28  18
  19P LOSS WILD-TYPE 155  32
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                46                187 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                 32 
$`19P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       23.67         5.46        31.40        30.21        35.01        57.73 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A7CO TCGA-C5-A7X3 
       35.61         0.46        20.91        40.93       147.35         9.34 
TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DS-A0VN 
        2.73        45.83        99.91        23.51        27.52       118.65 
TCGA-EA-A1QT TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EK-A2IP 
       12.36        14.50         1.35        14.50         1.81         6.64 
TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RJ TCGA-EK-A3GJ TCGA-EX-A69L 
        0.43         1.45        16.08         1.18         0.10        19.79 
TCGA-FU-A23L TCGA-GH-A9DA TCGA-IR-A3LC TCGA-JW-A5VK TCGA-JX-A3PZ TCGA-JX-A5QV 
       23.84         9.01       117.40        20.48        21.11         7.99 
TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73S TCGA-RA-A741 TCGA-VS-A8EB TCGA-VS-A8EJ 
        2.96         3.39        10.39         3.88        10.03        19.96 
TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A957 
       39.78        16.64         4.73        42.08 

$`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-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       46.32        53.16        38.99         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-A7UC 
      154.32       101.82       134.33        15.48        20.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI 
       85.55        60.69        94.95        13.61        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       75.78         6.12        20.91         4.47         1.12        58.88 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       50.76        44.94        40.04        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99        22.98        16.83        16.18        17.52 
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-A3QE TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       13.05         1.18         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-A5ZF 
       14.89         1.48        13.91        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       13.58        13.48         0.36        12.59        45.96        26.27 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC 
        1.51         0.59         0.59         0.13         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-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-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         4.73         1.22         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-HG-A9SC 
        1.35         1.32         1.97         1.12        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW 
        5.13         6.71       195.85        30.31        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         5.49        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       13.35        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
        5.88         6.25        19.59        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL 
       61.28        34.52        29.03        20.22        14.07        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       32.15        46.03        23.28        11.51        49.55        31.27 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       23.24        44.88        42.58        43.82        39.35        38.96 
TCGA-WL-A834 
       18.05 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.10               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            147.35             195.85 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             16.36              15.58 
[1] "0.1 - 147.3 (16.4)" "0.0 - 195.8 (15.6)"
[1] "hr=" "2.5"
D74V2, continuous
                    vv
clus                 T1 T2 T3+T4
  19P LOSS MUTATED   24  8     2
  19P LOSS WILD-TYPE 97 42     9
D74V3, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                  24                 97
  T2                   8                 42
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   23  5
  19P LOSS WILD-TYPE 88 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     23    5
  19P LOSS WILD-TYPE   88   42
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               23                 88
  1                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19P LOSS MUTATED   17  2 16
  19P LOSS WILD-TYPE 74  6 77
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               17                 74
  M1                2                  6
  MX               16                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED               1                               42
  19P LOSS WILD-TYPE             4                              155
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19P LOSS MUTATED                                               0
  19P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19P LOSS MUTATED                                     4
  19P LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19P LOSS MUTATED                                           0
  19P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19P LOSS MUTATED                                              2
  19P LOSS WILD-TYPE                                            4
D74V6, multiclass
                                               clus
vv                                              19P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            42
  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                                              19P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  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"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     8  41
  19P LOSS WILD-TYPE  22 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8   41
  19P LOSS WILD-TYPE   22  167
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 8                 22
  YES               41                167
[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                                8    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED                           4
  19P LOSS WILD-TYPE                        20
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    41
  19P LOSS WILD-TYPE                                         0   128
D74V10, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                4                 20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   41                128
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2  30
  19P LOSS WILD-TYPE  14 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   30
  19P LOSS WILD-TYPE   14  119
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               30                119
[1] 2 2
[1] FALSE
D74V12, continuous
D74V13, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   14  7
  19P LOSS WILD-TYPE 57 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     14    7
  19P LOSS WILD-TYPE   57   18
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  TUMOR FREE               14                 57
  WITH TUMOR                7                 18
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  19P LOSS MUTATED        6      0       1      2       2            37       1
  19P LOSS WILD-TYPE     17      5       0      8       5           141      13
D74V14, multiclass
               clus
vv              19P LOSS MUTATED 19P LOSS WILD-TYPE
  BRAZIL                       6                 17
  CANADA                       0                  5
  NIGERIA                      1                  0
  RUSSIA                       2                  8
  UKRAINE                      2                  5
  UNITED STATES               37                141
  VIETNAM                      1                 13
[1] 7 2
[1] 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 18 24  0  4
  19P LOSS WILD-TYPE 16 88 73  1 10
D74V15, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  G1                1                 16
  G2               18                 88
  G3               24                 73
  G4                0                  1
  GX                4                 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"
D74V16, continuous
D74V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19P LOSS MUTATED                                             5
  19P LOSS WILD-TYPE                                          26
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19P LOSS MUTATED                9                  23
  19P LOSS WILD-TYPE             43                  89
D74V18, multiclass
                                                 clus
vv                                                19P 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                                                 9
  LIFELONG NON-SMOKER                                           23
                                                 clus
vv                                                19P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  43
  LIFELONG NON-SMOKER                                             89
[1] 5 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
D74V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  19P LOSS MUTATED             5       15             3        3
  19P LOSS WILD-TYPE          14       60             9        9
D74V21, multiclass
               clus
vv              19P LOSS MUTATED 19P LOSS WILD-TYPE
  COMBINATION                  5                 14
  EXTERNAL                    15                 60
  EXTERNAL BEAM                3                  9
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V22, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    7  0
  19P LOSS WILD-TYPE 18  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7    0
  19P LOSS WILD-TYPE   18    3
                         clus
vv                        19P LOSS MUTATED 19P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   7                 18
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  19P LOSS MUTATED                    0                0                   6
  19P LOSS WILD-TYPE                  2                2                  22
                    vv
clus                 REGIONAL SITE
  19P LOSS MUTATED               3
  19P LOSS WILD-TYPE            13
D74V23, multiclass
                     clus
vv                    19P LOSS MUTATED 19P LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                6                 22
  REGIONAL SITE                      3                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V24, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    7  0
  19P LOSS WILD-TYPE 27  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7    0
  19P LOSS WILD-TYPE   27    3
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  CGY                7                 27
  GY                 0                  3
[1] 2 2
[1] FALSE
D74V25, continuous
D74V26, continuous
D74V27, continuous
D74V28, continuous
D74V29, continuous
D74V30, 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                         7                       0
  19P LOSS WILD-TYPE                      22                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19P LOSS MUTATED                         0
  19P LOSS WILD-TYPE                       7
D74V31, multiclass
                                     clus
vv                                    19P LOSS MUTATED 19P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            7                 22
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  19P LOSS MUTATED                                               1
  19P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  19P LOSS MUTATED                                                1
  19P LOSS WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19P LOSS MUTATED                                                                                  13
  19P LOSS WILD-TYPE                                                                                55
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19P LOSS MUTATED                                                                                             19
  19P LOSS WILD-TYPE                                                                                           86
D74V32, multiclass
                                                                                              clus
vv                                                                                             19P 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)                          13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               19
                                                                                              clus
vv                                                                                             19P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            55
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V33, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   13 11
  19P LOSS WILD-TYPE 55 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     13   11
  19P LOSS WILD-TYPE   55   59
         clus
vv        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ABSENT                13                 55
  PRESENT               11                 59
[1] 2 2
[1] FALSE
D74V34, continuous
D74V35, continuous
D74V36, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    8 19
  19P LOSS WILD-TYPE 35 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8   19
  19P LOSS WILD-TYPE   35   75
                                          clus
vv                                         19P LOSS MUTATED 19P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    8                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               19                 75
[1] 2 2
[1] FALSE
D74V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19P LOSS MUTATED              2           8         11
  19P LOSS WILD-TYPE            8          41         46
D74V38, multiclass
              clus
vv             19P LOSS MUTATED 19P LOSS WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                 8                 41
  NEVER USED                 11                 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"
D74V39, continuous
D74V40, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   16  5
  19P LOSS WILD-TYPE 73 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     16    5
  19P LOSS WILD-TYPE   73   11
         clus
vv        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ABSENT                16                 73
  PRESENT                5                 11
[1] 2 2
[1] FALSE
D74V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  19P LOSS MUTATED     0    0   6   14    4  0   1    2    1   4  0   2  0   0
  19P LOSS WILD-TYPE   1    1  24   51   20  4   7    5    8  18  1   6  2   1
                    vv
clus                 TX
  19P LOSS MUTATED    2
  19P LOSS WILD-TYPE 12
D74V42, multiclass
      clus
vv     19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 6                 24
  T1B1               14                 51
  T1B2                4                 20
  T2                  0                  4
  T2A                 1                  7
  T2A1                2                  5
  T2A2                1                  8
  T2B                 4                 18
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  19P LOSS MUTATED         1        0         0         0        5        21
  19P LOSS WILD-TYPE       3        2         1         1       26        48
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  19P LOSS MUTATED           6        0         1          2          1
  19P LOSS WILD-TYPE        26        3         5          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  19P LOSS MUTATED           6         0          5         0         0
  19P LOSS WILD-TYPE        21         1         29         3         7
D74V44, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  5                 26
  STAGE IB1                21                 48
  STAGE IB2                 6                 26
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                 6                 21
  STAGE III                 0                  1
  STAGE IIIB                5                 29
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    15   8
  19Q LOSS WILD-TYPE 168  42
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                23                210 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 42 
$`19Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A7X8 
       31.40        30.21        35.01         0.46        20.91         2.73 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EK-A2IP TCGA-EK-A3GJ 
       99.91        23.51       118.65        12.36         6.64         0.10 
TCGA-FU-A23L TCGA-GH-A9DA TCGA-IR-A3LC TCGA-JW-A5VK TCGA-JX-A3Q8 TCGA-JX-A5QV 
       23.84         9.01       117.40        20.48        30.31         7.99 
TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8QH TCGA-VS-A957 
        3.39        20.22        19.96        39.78        42.08 

$`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       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
       85.55        60.69        94.95         9.34        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
       45.83         8.35        75.78        27.52         6.12        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
        4.47         1.12        58.88        50.76        44.94        40.04 
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-A3HQ 
       16.83        16.18        17.52         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-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        15.02        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         1.51         0.43         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.13        16.08         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-A3GK 
        1.18        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-A69L 
        0.03        20.35         7.92         6.94        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         4.73         1.22         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-HG-A9SC 
        1.35         1.32         1.97         1.12        25.41         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        10.06 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AW 
        5.13         6.71        21.11       195.85        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI 
        0.07         0.30         0.82         0.20        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
        5.42        29.72         0.07         4.34         5.49         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        13.35        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         5.88         6.25        10.39        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        61.28        10.03        34.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       29.03        14.07        53.52        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       11.51        49.55        31.27        16.64         4.73        23.24 
TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       44.88        42.58        43.82        39.35        38.96        18.05 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.10               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            118.65             195.85 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             20.91              15.25 
[1] "0.1 - 118.7 (20.9)" "0.0 - 195.8 (15.2)"
[1] "hr=" "1.5"
D75V2, continuous
                    vv
clus                  T1  T2 T3+T4
  19Q LOSS MUTATED    12   3     2
  19Q LOSS WILD-TYPE 109  47     9
D75V3, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                  12                109
  T2                   3                 47
  T3+T4                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    11   2
  19Q LOSS WILD-TYPE 100  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     11    2
  19Q LOSS WILD-TYPE  100   45
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               11                100
  1                2                 45
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19Q LOSS MUTATED    7  1 10
  19Q LOSS WILD-TYPE 84  7 83
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                7                 84
  M1                1                  7
  MX               10                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED               0                               19
  19Q LOSS WILD-TYPE             5                              178
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19Q LOSS MUTATED                                               0
  19Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19Q LOSS MUTATED                                     4
  19Q LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19Q LOSS MUTATED                                           0
  19Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19Q LOSS MUTATED                                              2
  19Q LOSS WILD-TYPE                                            4
D75V6, multiclass
                                               clus
vv                                              19Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            19
  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                                              19Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             178
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  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"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5  20
  19Q LOSS WILD-TYPE  25 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5   20
  19Q LOSS WILD-TYPE   25  188
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 5                 25
  YES               20                188
[1] 2 2
[1] FALSE
D75V8, continuous
D75V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     1
  19Q LOSS WILD-TYPE                                8    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED                           2
  19Q LOSS WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           1    20
  19Q LOSS WILD-TYPE                                         0   149
D75V10, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                2                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   20                149
[1] 5 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  11
  19Q LOSS WILD-TYPE  15 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   11
  19Q LOSS WILD-TYPE   15  138
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               11                138
[1] 2 2
[1] FALSE
D75V12, continuous
D75V13, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    8  4
  19Q LOSS WILD-TYPE 63 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8    4
  19Q LOSS WILD-TYPE   63   21
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  TUMOR FREE                8                 63
  WITH TUMOR                4                 21
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  19Q LOSS MUTATED        4      0       0      1       0            20       0
  19Q LOSS WILD-TYPE     19      5       1      9       7           158      14
D75V14, multiclass
               clus
vv              19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  BRAZIL                       4                 19
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  7
  UNITED STATES               20                158
  VIETNAM                      0                 14
[1] 7 2
[1] 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 10 14  0  1
  19Q LOSS WILD-TYPE 17 96 83  1 13
D75V15, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  G1                0                 17
  G2               10                 96
  G3               14                 83
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V16, continuous
D75V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19Q LOSS MUTATED                                             0
  19Q LOSS WILD-TYPE                                          31
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19Q LOSS MUTATED                5                  15
  19Q LOSS WILD-TYPE             47                  97
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                                                 5
  LIFELONG NON-SMOKER                                           15
                                                 clus
vv                                                19Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  47
  LIFELONG NON-SMOKER                                             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"
D75V19, continuous
D75V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  19Q LOSS MUTATED             2        9             3        1
  19Q LOSS WILD-TYPE          17       66             9       11
D75V21, multiclass
               clus
vv              19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COMBINATION                  2                 17
  EXTERNAL                     9                 66
  EXTERNAL BEAM                3                  9
  INTERNAL                     1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V22, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4  0
  19Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    0
  19Q LOSS WILD-TYPE   21    3
                         clus
vv                        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  19Q LOSS MUTATED                    0                0                   5
  19Q LOSS WILD-TYPE                  2                2                  23
                    vv
clus                 REGIONAL SITE
  19Q LOSS MUTATED               2
  19Q LOSS WILD-TYPE            14
D75V23, multiclass
                     clus
vv                    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                5                 23
  REGIONAL SITE                      2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V24, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    6  0
  19Q LOSS WILD-TYPE 28  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    0
  19Q LOSS WILD-TYPE   28    3
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CGY                6                 28
  GY                 0                  3
[1] 2 2
[1] FALSE
D75V25, continuous
D75V26, continuous
D75V27, continuous
D75V28, continuous
D75V29, continuous
D75V30, 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                         5                       0
  19Q LOSS WILD-TYPE                      24                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19Q LOSS MUTATED                         0
  19Q LOSS WILD-TYPE                       7
D75V31, multiclass
                                     clus
vv                                    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            5                 24
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  19Q LOSS MUTATED                                               1
  19Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  19Q LOSS MUTATED                                                1
  19Q LOSS WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19Q LOSS MUTATED                                                                                  11
  19Q LOSS WILD-TYPE                                                                                57
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19Q LOSS MUTATED                                                                                              6
  19Q LOSS WILD-TYPE                                                                                           99
D75V32, multiclass
                                                                                              clus
vv                                                                                             19Q 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)                          11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                6
                                                                                              clus
vv                                                                                             19Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V33, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    9  4
  19Q LOSS WILD-TYPE 59 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      9    4
  19Q LOSS WILD-TYPE   59   66
         clus
vv        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ABSENT                 9                 59
  PRESENT                4                 66
[1] 2 2
[1] FALSE
D75V34, continuous
D75V35, continuous
D75V36, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  5
  19Q LOSS WILD-TYPE 40 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    5
  19Q LOSS WILD-TYPE   40   89
                                          clus
vv                                         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                5                 89
[1] 2 2
[1] FALSE
D75V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19Q LOSS MUTATED              1           4          6
  19Q LOSS WILD-TYPE            9          45         51
D75V38, multiclass
              clus
vv             19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 4                 45
  NEVER USED                  6                 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"
D75V39, continuous
D75V40, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   11  1
  19Q LOSS WILD-TYPE 78 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     11    1
  19Q LOSS WILD-TYPE   78   15
         clus
vv        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ABSENT                11                 78
  PRESENT                1                 15
[1] 2 2
[1] FALSE
D75V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  19Q LOSS MUTATED     0    0   3    7    2  0   1    1    0   1  0   2  0   0
  19Q LOSS WILD-TYPE   1    1  27   58   22  4   7    6    9  21  1   6  2   1
                    vv
clus                 TX
  19Q LOSS MUTATED    2
  19Q LOSS WILD-TYPE 12
D75V42, multiclass
      clus
vv     19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 3                 27
  T1B1                7                 58
  T1B2                2                 22
  T2                  0                  4
  T2A                 1                  7
  T2A1                1                  6
  T2A2                0                  9
  T2B                 1                 21
  T3                  0                  1
  T3B                 2                  6
  T4                  0                  2
  TIS                 0                  1
  TX                  2                 12
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  19Q LOSS MUTATED         1        0         0         0        2        13
  19Q LOSS WILD-TYPE       3        2         1         1       29        56
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  19Q LOSS MUTATED           2        0         1          1          0
  19Q LOSS WILD-TYPE        30        3         5          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  19Q LOSS MUTATED           2         0          2         0         0
  19Q LOSS WILD-TYPE        25         1         32         3         7
D75V44, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  2                 29
  STAGE IB1                13                 56
  STAGE IB2                 2                 30
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 2                 25
  STAGE III                 0                  1
  STAGE IIIB                2                 32
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    13   4
  20P LOSS WILD-TYPE 170  46
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                17                216 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 46 
$`20P LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A1ME TCGA-C5-A8XH TCGA-DG-A2KK TCGA-EA-A1QT TCGA-EK-A2H0 
       49.48        57.73        45.83        50.76        12.36        45.96 
TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-FU-A770 TCGA-GH-A9DA TCGA-IR-A3LB TCGA-JW-A5VI 
        7.92         0.66         1.12         9.01        66.81        24.56 
TCGA-JX-A5QV TCGA-MY-A913 TCGA-UC-A7PD TCGA-VS-A8Q9 TCGA-VS-A94Y 
        7.99         5.49        11.67        46.03         4.73 

$`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-A1MF 
       67.46        31.40        46.32        30.21        35.01        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-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       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34        13.61         2.73        50.99         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52         6.12        20.91         4.47 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        58.88        44.94        40.04        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-A3HQ TCGA-EA-A3HR 
       16.18        17.52         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        15.02        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.58        13.48         0.36        12.59        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.43         0.59         0.59         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
       16.08         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-A3GK 
       23.70         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03        20.35         6.94        14.70        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
        4.73         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-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       147.39       137.16       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        26.56        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       195.85        30.31        11.28         0.89         0.07 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.30         0.82         0.20        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        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        5.88         6.25        10.39        19.59         3.88        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        61.28        10.03        34.52        29.03        20.22 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC 
       14.07        19.96        53.52        32.15        23.28        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       49.55        39.78        31.27        16.64        23.24        44.88 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       42.58        42.08        43.82        39.35        38.96        18.05 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.66               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             66.81             195.85 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            12.360             15.915 
[1] "0.7 - 66.8 (12.4)"  "0.0 - 195.8 (15.9)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                  T1  T2 T3+T4
  20P LOSS MUTATED    11   4     0
  20P LOSS WILD-TYPE 110  46    11
D76V3, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                  11                110
  T2                   4                 46
  T3+T4                0                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V4, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    10   4
  20P LOSS WILD-TYPE 101  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     10    4
  20P LOSS WILD-TYPE  101   43
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               10                101
  1                4                 43
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20P LOSS MUTATED    8  1  8
  20P LOSS WILD-TYPE 83  7 85
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                8                 83
  M1                1                  7
  MX                8                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED               0                               15
  20P LOSS WILD-TYPE             5                              182
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20P LOSS MUTATED                                               1
  20P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20P LOSS MUTATED                                     3
  20P LOSS WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20P LOSS MUTATED                                           0
  20P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20P LOSS MUTATED                                              0
  20P LOSS WILD-TYPE                                            6
D76V6, multiclass
                                               clus
vv                                              20P 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                                              20P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             182
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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     1  18
  20P LOSS WILD-TYPE  29 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   18
  20P LOSS WILD-TYPE   29  190
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                 29
  YES               18                190
[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                                6    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED                           1
  20P LOSS WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    14
  20P LOSS WILD-TYPE                                         1   155
D76V10, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                1                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                155
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  10
  20P LOSS WILD-TYPE  14 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   10
  20P LOSS WILD-TYPE   14  139
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               10                139
[1] 2 2
[1] FALSE
D76V12, continuous
D76V13, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    5  1
  20P LOSS WILD-TYPE 66 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5    1
  20P LOSS WILD-TYPE   66   24
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  TUMOR FREE                5                 66
  WITH TUMOR                1                 24
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  20P LOSS MUTATED        2      1       0      1       0            14       1
  20P LOSS WILD-TYPE     21      4       1      9       7           164      13
D76V14, multiclass
               clus
vv              20P LOSS MUTATED 20P LOSS WILD-TYPE
  BRAZIL                       2                 21
  CANADA                       1                  4
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  7
  UNITED STATES               14                164
  VIETNAM                      1                 13
[1] 7 2
[1] 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    2  7  8  0  1
  20P LOSS WILD-TYPE 15 99 89  1 13
D76V15, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  G1                2                 15
  G2                7                 99
  G3                8                 89
  G4                0                  1
  GX                1                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V16, continuous
D76V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20P LOSS MUTATED                                             4
  20P LOSS WILD-TYPE                                          27
                    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                                                 1
  20P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20P LOSS MUTATED                6                   5
  20P LOSS WILD-TYPE             46                 107
D76V18, multiclass
                                                 clus
vv                                                20P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 6
  LIFELONG NON-SMOKER                                            5
                                                 clus
vv                                                20P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  46
  LIFELONG NON-SMOKER                                            107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V19, continuous
D76V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  20P LOSS MUTATED             0        5             1        3
  20P LOSS WILD-TYPE          19       70            11        9
D76V21, multiclass
               clus
vv              20P LOSS MUTATED 20P LOSS WILD-TYPE
  COMBINATION                  0                 19
  EXTERNAL                     5                 70
  EXTERNAL BEAM                1                 11
  INTERNAL                     3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V22, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    0  1
  20P LOSS WILD-TYPE 25  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    1
  20P LOSS WILD-TYPE   25    2
                         clus
vv                        20P LOSS MUTATED 20P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   0                 25
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  20P LOSS MUTATED                    0                0                   3
  20P LOSS WILD-TYPE                  2                2                  25
                    vv
clus                 REGIONAL SITE
  20P LOSS MUTATED               0
  20P LOSS WILD-TYPE            16
D76V23, multiclass
                     clus
vv                    20P LOSS MUTATED 20P LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   0                  2
  PRIMARY TUMOR FIELD                3                 25
  REGIONAL SITE                      0                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V24, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    2  1
  20P LOSS WILD-TYPE 32  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    1
  20P LOSS WILD-TYPE   32    2
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  CGY                2                 32
  GY                 1                  2
[1] 2 2
[1] FALSE
D76V25, continuous
D76V26, continuous
D76V27, continuous
D76V28, continuous
D76V29, continuous
D76V30, 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                         3                       0
  20P LOSS WILD-TYPE                      26                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20P LOSS MUTATED                         0
  20P LOSS WILD-TYPE                       7
D76V31, multiclass
                                     clus
vv                                    20P LOSS MUTATED 20P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            3                 26
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  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                                             16
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20P LOSS MUTATED                                                                                   5
  20P LOSS WILD-TYPE                                                                                63
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20P LOSS MUTATED                                                                                             10
  20P LOSS WILD-TYPE                                                                                           95
D76V32, 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)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               10
                                                                                              clus
vv                                                                                             20P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            63
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V33, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    6  5
  20P LOSS WILD-TYPE 62 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    5
  20P LOSS WILD-TYPE   62   65
         clus
vv        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ABSENT                 6                 62
  PRESENT                5                 65
[1] 2 2
[1] FALSE
D76V34, continuous
D76V35, continuous
D76V36, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3  6
  20P LOSS WILD-TYPE 40 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    6
  20P LOSS WILD-TYPE   40   88
                                          clus
vv                                         20P LOSS MUTATED 20P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                6                 88
[1] 2 2
[1] FALSE
D76V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20P LOSS MUTATED              2           5          3
  20P LOSS WILD-TYPE            8          44         54
D76V38, multiclass
              clus
vv             20P LOSS MUTATED 20P LOSS WILD-TYPE
  CURRENT USER                2                  8
  FORMER USER                 5                 44
  NEVER USED                  3                 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"
D76V39, continuous
D76V40, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8  1
  20P LOSS WILD-TYPE 81 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    1
  20P LOSS WILD-TYPE   81   15
         clus
vv        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ABSENT                 8                 81
  PRESENT                1                 15
[1] 2 2
[1] FALSE
D76V41, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 11 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  20P LOSS MUTATED     0    0   4    6    1  0   0    0    1   3  0   0  0   1
  20P LOSS WILD-TYPE   1    1  26   59   23  4   8    7    8  19  1   8  2   0
                    vv
clus                 TX
  20P LOSS MUTATED    1
  20P LOSS WILD-TYPE 13
D76V42, multiclass
      clus
vv     20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 4                 26
  T1B1                6                 59
  T1B2                1                 23
  T2                  0                  4
  T2A                 0                  8
  T2A1                0                  7
  T2A2                1                  8
  T2B                 3                 19
  T3                  0                  1
  T3B                 0                  8
  T4                  0                  2
  TIS                 1                  0
  TX                  1                 13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  20P LOSS MUTATED         0        0         0         0        3         7
  20P LOSS WILD-TYPE       4        2         1         1       28        62
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  20P LOSS MUTATED           1        0         1          0          0
  20P LOSS WILD-TYPE        31        3         5          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  20P LOSS MUTATED           3         0          4         0         0
  20P LOSS WILD-TYPE        24         1         30         3         7
D76V44, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 28
  STAGE IB1                 7                 62
  STAGE IB2                 1                 31
  STAGE II                  0                  3
  STAGE IIA                 1                  5
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 3                 24
  STAGE III                 0                  1
  STAGE IIIB                4                 30
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   4
  20Q LOSS WILD-TYPE 180  46
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                226 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                 46 
$`20Q LOSS MUTATED`
TCGA-C5-A8XH TCGA-HG-A2PA TCGA-JX-A5QV TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A94Y 
       45.83        25.41         7.99        11.67        10.03         4.73 
TCGA-VS-A9U5 
       38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43         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       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
       60.69        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35        75.78        99.91        23.51        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91         4.47         1.12        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        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        17.52         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-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91        15.02        14.99        14.96        13.58        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
        0.36        12.59        45.96        26.27         6.64         1.51 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.59         1.45         0.13        16.08 
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        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.73         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-GH-A9DA TCGA-HG-A9SC 
        1.35         1.32         1.97         1.12         9.01         7.13 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        10.06         5.13         6.71        21.11       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       30.31        11.28         0.89         0.07         0.30         0.82 
TCGA-LP-A7HU TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.20        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        4.34         5.49         2.96        15.58        13.35        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        3.39        16.14        17.56        14.07        15.88         5.88 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG 
        6.25        10.39        19.59         3.88        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       61.28        34.52        29.03        20.22        14.07        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       53.52        32.15        46.03        23.28        11.51        49.55 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       39.78        31.27        16.64        23.24        44.88        42.58 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-WL-A834 
       42.08        43.82        39.35        18.05 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              4.73               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             45.83             195.85 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            11.670             15.915 
[1] "4.7 - 45.8 (11.7)"  "0.0 - 195.8 (15.9)"
[1] "hr=" "3.4"
D77V2, continuous
                    vv
clus                  T1  T2 T3+T4
  20Q LOSS MUTATED     4   2     1
  20Q LOSS WILD-TYPE 117  48    10
D77V3, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                   4                117
  T2                   2                 48
  T3+T4                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   0
  20Q LOSS WILD-TYPE 107  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    0
  20Q LOSS WILD-TYPE  107   47
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                4                107
  1                0                 47
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20Q LOSS MUTATED    3  1  3
  20Q LOSS WILD-TYPE 88  7 90
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                3                 88
  M1                1                  7
  MX                3                 90
[1] 3 2
[1] 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                                8
  20Q LOSS WILD-TYPE             5                              189
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20Q LOSS MUTATED                                               0
  20Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20Q LOSS MUTATED                                     0
  20Q LOSS WILD-TYPE                                  22
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20Q LOSS MUTATED                                           0
  20Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20Q LOSS MUTATED                                              0
  20Q LOSS WILD-TYPE                                            6
D77V6, multiclass
                                               clus
vv                                              20Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             8
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              20Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             189
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           22
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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   8
  20Q LOSS WILD-TYPE  30 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    8
  20Q LOSS WILD-TYPE   30  200
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                 30
  YES                8                200
[1] 2 2
[1] FALSE
D77V8, continuous
D77V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  1     0
  20Q LOSS WILD-TYPE                                7    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED                           0
  20Q LOSS WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0     7
  20Q LOSS WILD-TYPE                                         1   162
D77V10, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    0                 18
  BLACK OR AFRICAN AMERICAN                                0                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                162
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   3
  20Q LOSS WILD-TYPE  16 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    3
  20Q LOSS WILD-TYPE   16  146
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO                3                146
[1] 2 2
[1] FALSE
D77V12, continuous
D77V13, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  0
  20Q LOSS WILD-TYPE 70 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    0
  20Q LOSS WILD-TYPE   70   25
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  TUMOR FREE                1                 70
  WITH TUMOR                0                 25
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  20Q LOSS MUTATED        3      0       0      0       0             5       0
  20Q LOSS WILD-TYPE     20      5       1     10       7           173      14
D77V14, multiclass
               clus
vv              20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  BRAZIL                       3                 20
  CANADA                       0                  5
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  7
  UNITED STATES                5                173
  VIETNAM                      0                 14
[1] 7 2
[1] 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   2   0   2
  20Q LOSS WILD-TYPE  17 103  95   1  12
D77V15, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  G1                0                 17
  G2                3                103
  G3                2                 95
  G4                0                  1
  GX                2                 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"
D77V16, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 33 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1ME         TCGA-C5-A1MF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A2M2         TCGA-C5-A3HD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-C5-A907 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DS-A3LQ         TCGA-EK-A2RA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EX-A69M         TCGA-FU-A2QG         TCGA-FU-A3TX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-HM-A3JK         TCGA-HM-A4S6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-MU-A5YI         TCGA-MU-A8JM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73S         TCGA-RA-A741 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A8QF         TCGA-VS-A94Z         TCGA-WL-A834 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20Q LOSS MUTATED                                             1
  20Q LOSS WILD-TYPE                                          30
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20Q LOSS MUTATED                4                   2
  20Q LOSS WILD-TYPE             48                 110
D77V18, multiclass
                                                 clus
vv                                                20Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                            2
                                                 clus
vv                                                20Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  48
  LIFELONG NON-SMOKER                                            110
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V19, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 65 
        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-C5-A8XI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A8YQ         TCGA-C5-A8YT         TCGA-C5-A8ZZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A907         TCGA-DG-A2KK         TCGA-DR-A0ZM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-EA-A556         TCGA-EK-A2RA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3TX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         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-JW-AAVH         TCGA-JX-A3Q0         TCGA-MU-A5YI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A8EH         TCGA-VS-A8QF         TCGA-VS-A8QM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-WL-A834 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  20Q LOSS MUTATED             0        3             0        2
  20Q LOSS WILD-TYPE          19       72            12       10
D77V21, multiclass
               clus
vv              20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COMBINATION                  0                 19
  EXTERNAL                     3                 72
  EXTERNAL BEAM                0                 12
  INTERNAL                     2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V22, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  0
  20Q LOSS WILD-TYPE 25  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE   25    3
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  20Q LOSS MUTATED                    0                0                   2
  20Q LOSS WILD-TYPE                  2                2                  26
                    vv
clus                 REGIONAL SITE
  20Q LOSS MUTATED               0
  20Q LOSS WILD-TYPE            16
D77V23, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 46 
        TCGA-C5-A0TN         TCGA-C5-A1BF         TCGA-C5-A1BQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LZ         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-A8XJ         TCGA-C5-A8XK         TCGA-C5-A8YQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A8YT         TCGA-C5-A8ZZ         TCGA-C5-A907 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DG-A2KL         TCGA-DS-A7WF         TCGA-EX-A3L1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-HM-A3JJ         TCGA-HM-A4S6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-JW-A5VG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MY-A913         TCGA-R2-A69V         TCGA-UC-A7PG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A8EC         TCGA-VS-A8EG         TCGA-VS-A8EH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A8EI         TCGA-VS-A8EL         TCGA-VS-A8Q8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A8Q9         TCGA-VS-A8QC         TCGA-VS-A8QF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A8QH         TCGA-VS-A94X         TCGA-VS-A94Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A954         TCGA-VS-A957         TCGA-VS-A958 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A959 
"20Q LOSS WILD-TYPE" 
D77V24, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  0
  20Q LOSS WILD-TYPE 32  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    0
  20Q LOSS WILD-TYPE   32    3
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CGY                2                 32
  GY                 0                  3
[1] 2 2
[1] FALSE
D77V25, continuous
D77V26, continuous
D77V27, continuous
D77V28, continuous
D77V29, continuous
D77V30, continuous
                    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                         2                       0
  20Q LOSS WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20Q LOSS MUTATED                         0
  20Q LOSS WILD-TYPE                       7
D77V31, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 43 
        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-A1M5         TCGA-C5-A1M7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1M9         TCGA-C5-A1ME 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MJ         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-A2M1         TCGA-C5-A3HE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CJ         TCGA-C5-A7UC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DG-A2KL         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-EA-A50E         TCGA-EK-A2RN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-EX-A1H5         TCGA-EX-A449 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-HM-A4S6         TCGA-IR-A3LH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-MU-A8JM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A8QA 
"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                                                1
  20Q LOSS WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20Q LOSS MUTATED                                                                                   0
  20Q LOSS WILD-TYPE                                                                                68
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20Q LOSS MUTATED                                                                                              5
  20Q LOSS WILD-TYPE                                                                                          100
D77V32, multiclass
                                                                                              clus
vv                                                                                             20Q 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)                5
                                                                                              clus
vv                                                                                             20Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V33, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 67 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE   67   68
         clus
vv        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ABSENT                 1                 67
  PRESENT                2                 68
[1] 2 2
[1] FALSE
D77V34, continuous
D77V35, continuous
D77V36, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  1
  20Q LOSS WILD-TYPE 40 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    1
  20Q LOSS WILD-TYPE   40   93
                                          clus
vv                                         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                 93
[1] 2 2
[1] FALSE
D77V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20Q LOSS MUTATED              1           1          3
  20Q LOSS WILD-TYPE            9          48         54
D77V38, multiclass
              clus
vv             20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CURRENT USER                1                  9
  FORMER USER                 1                 48
  NEVER USED                  3                 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"
D77V39, continuous
D77V40, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  1
  20Q LOSS WILD-TYPE 88 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    1
  20Q LOSS WILD-TYPE   88   15
         clus
vv        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ABSENT                 1                 88
  PRESENT                1                 15
[1] 2 2
[1] FALSE
D77V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  20Q LOSS MUTATED     0    0   1    2    1  0   0    0    0   2  0   1  0   0
  20Q LOSS WILD-TYPE   1    1  29   63   23  4   8    7    9  20  1   7  2   1
                    vv
clus                 TX
  20Q LOSS MUTATED    0
  20Q LOSS WILD-TYPE 14
D77V42, multiclass
      clus
vv     20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 1                 29
  T1B1                2                 63
  T1B2                1                 23
  T2                  0                  4
  T2A                 0                  8
  T2A1                0                  7
  T2A2                0                  9
  T2B                 2                 20
  T3                  0                  1
  T3B                 1                  7
  T4                  0                  2
  TIS                 0                  1
  TX                  0                 14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  20Q LOSS MUTATED         0        0         0         0        1         2
  20Q LOSS WILD-TYPE       4        2         1         1       30        67
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  20Q LOSS MUTATED           1        0         0          0          0
  20Q LOSS WILD-TYPE        31        3         6          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  20Q LOSS MUTATED           2         0          2         0         0
  20Q LOSS WILD-TYPE        25         1         32         3         7
D77V44, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  1                 30
  STAGE IB1                 2                 67
  STAGE IB2                 1                 31
  STAGE II                  0                  3
  STAGE IIA                 0                  6
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 2                 25
  STAGE III                 0                  1
  STAGE IIIB                2                 32
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    29  12
  21Q LOSS WILD-TYPE 154  38
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                41                192 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                12                 38 
$`21Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A2LT 
       57.04        23.67        11.44        35.01         0.46        73.18 
TCGA-C5-A2LV TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KJ 
       73.45         9.34        45.83        23.51        27.52        58.88 
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 
       87.75         2.66         1.32         1.35        14.50        14.89 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.36        12.59         1.51         1.45         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         9.44        27.42 
TCGA-LP-A7HU TCGA-PN-A8MA TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI 
        0.20         2.96        12.16        10.03        20.22        14.07 
TCGA-VS-A8Q9 TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       46.03         4.73        42.08        39.35        38.96 

$`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-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX 
        2.43        20.91        40.93         3.58        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43         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       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95        13.61         2.73        50.99         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       99.91         6.12        20.91         4.47         1.12        50.76 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       44.94        40.04        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        17.52         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        15.02        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM 
       13.48        45.96        26.27         6.64         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         0.13        16.08         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.36         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03        20.35         7.92        14.70        19.79         6.12 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        4.73         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
        1.97         1.12         9.01        25.41         7.13        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        10.06         5.13         6.71 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       195.85        30.31         7.99        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.07         0.30         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         5.49        15.58        13.35 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         3.39        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.88         6.25        10.39        19.59         3.88        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL 
       93.99        61.28        34.52        29.03        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        23.28        11.51        49.55        39.78        31.27 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-WL-A834 
       16.64        23.24        44.88        42.58        43.82        18.05 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.20               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             87.75             195.85 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            14.500             16.015 
[1] "0.2 - 87.8 (14.5)"  "0.0 - 195.8 (16.0)"
[1] "hr=" "1.8"
D78V2, continuous
                    vv
clus                  T1  T2 T3+T4
  21Q LOSS MUTATED    20  11     5
  21Q LOSS WILD-TYPE 101  39     6
D78V3, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                  20                101
  T2                  11                 39
  T3+T4                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V4, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   19  9
  21Q LOSS WILD-TYPE 92 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     19    9
  21Q LOSS WILD-TYPE   92   38
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               19                 92
  1                9                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED   18  2 17
  21Q LOSS WILD-TYPE 73  6 76
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               18                 73
  M1                2                  6
  MX               17                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED               1                               36
  21Q LOSS WILD-TYPE             4                              161
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  21Q LOSS MUTATED                                               0
  21Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  21Q LOSS MUTATED                                     4
  21Q LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  21Q LOSS MUTATED                                           1
  21Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  21Q LOSS MUTATED                                              0
  21Q LOSS WILD-TYPE                                            6
D78V6, multiclass
                                               clus
vv                                              21Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            36
  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                                              21Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             161
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   6
[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  38
  21Q LOSS WILD-TYPE  26 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   38
  21Q LOSS WILD-TYPE   26  170
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                 26
  YES               38                170
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     3
  21Q LOSS WILD-TYPE                                7    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED                           8
  21Q LOSS WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           0    27
  21Q LOSS WILD-TYPE                                         1   142
D78V10, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                8                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   27                142
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  27
  21Q LOSS WILD-TYPE  15 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   27
  21Q LOSS WILD-TYPE   15  122
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               27                122
[1] 2 2
[1] FALSE
D78V12, continuous
D78V13, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   12  5
  21Q LOSS WILD-TYPE 59 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12    5
  21Q LOSS WILD-TYPE   59   20
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  TUMOR FREE               12                 59
  WITH TUMOR                5                 20
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  21Q LOSS MUTATED        8      1       1      3       1            26       2
  21Q LOSS WILD-TYPE     15      4       0      7       6           152      12
D78V14, multiclass
               clus
vv              21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  BRAZIL                       8                 15
  CANADA                       1                  4
  NIGERIA                      1                  0
  RUSSIA                       3                  7
  UKRAINE                      1                  6
  UNITED STATES               26                152
  VIETNAM                      2                 12
[1] 7 2
[1] 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    1 12 25  0  3
  21Q LOSS WILD-TYPE 16 94 72  1 11
D78V15, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  G1                1                 16
  G2               12                 94
  G3               25                 72
  G4                0                  1
  GX                3                 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"
D78V16, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 33 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1ME         TCGA-C5-A1MF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A2M2         TCGA-C5-A3HD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-C5-A907 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DS-A3LQ         TCGA-EK-A2RA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EX-A69M         TCGA-FU-A2QG         TCGA-FU-A3TX 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-HM-A3JK         TCGA-HM-A4S6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-MU-A5YI         TCGA-MU-A8JM 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73S         TCGA-RA-A741 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-VS-A8QF         TCGA-VS-A94Z         TCGA-WL-A834 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D78V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  21Q LOSS MUTATED                                             1
  21Q LOSS WILD-TYPE                                          30
                    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                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  21Q LOSS MUTATED               11                  20
  21Q LOSS WILD-TYPE             41                  92
D78V18, multiclass
                                                 clus
vv                                                21Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                11
  LIFELONG NON-SMOKER                                           20
                                                 clus
vv                                                21Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  41
  LIFELONG NON-SMOKER                                             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"
D78V19, continuous
D78V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  21Q LOSS MUTATED             0       17             4        0
  21Q LOSS WILD-TYPE          19       58             8       12
D78V21, multiclass
               clus
vv              21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COMBINATION                  0                 19
  EXTERNAL                    17                 58
  EXTERNAL BEAM                4                  8
  INTERNAL                     0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V22, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3  1
  21Q LOSS WILD-TYPE 22  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    1
  21Q LOSS WILD-TYPE   22    2
                         clus
vv                        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   3                 22
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  21Q LOSS MUTATED                    0                2                   9
  21Q LOSS WILD-TYPE                  2                0                  19
                    vv
clus                 REGIONAL SITE
  21Q LOSS MUTATED               3
  21Q LOSS WILD-TYPE            13
D78V23, multiclass
                     clus
vv                    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 0                  2
  LOCAL RECURRENCE                   2                  0
  PRIMARY TUMOR FIELD                9                 19
  REGIONAL SITE                      3                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V24, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   13  0
  21Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     13    0
  21Q LOSS WILD-TYPE   21    3
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CGY               13                 21
  GY                 0                  3
[1] 2 2
[1] FALSE
D78V25, continuous
D78V26, continuous
D78V27, continuous
D78V28, continuous
D78V29, continuous
D78V30, 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                         6                       0
  21Q LOSS WILD-TYPE                      23                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  21Q LOSS MUTATED                         0
  21Q LOSS WILD-TYPE                       7
D78V31, multiclass
                                     clus
vv                                    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                            6                 23
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  21Q LOSS MUTATED                                               0
  21Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  21Q LOSS MUTATED                                                2
  21Q LOSS WILD-TYPE                                             14
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  21Q LOSS MUTATED                                                                                  12
  21Q LOSS WILD-TYPE                                                                                56
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  21Q LOSS MUTATED                                                                                             20
  21Q LOSS WILD-TYPE                                                                                           85
D78V32, multiclass
                                                                                              clus
vv                                                                                             21Q 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)                          12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               20
                                                                                              clus
vv                                                                                             21Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V33, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   12 11
  21Q LOSS WILD-TYPE 56 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12   11
  21Q LOSS WILD-TYPE   56   59
         clus
vv        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ABSENT                12                 56
  PRESENT               11                 59
[1] 2 2
[1] FALSE
D78V34, continuous
D78V35, continuous
D78V36, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    5 20
  21Q LOSS WILD-TYPE 38 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5   20
  21Q LOSS WILD-TYPE   38   74
                                          clus
vv                                         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    5                 38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               20                 74
[1] 2 2
[1] FALSE
D78V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  21Q LOSS MUTATED              3           5         15
  21Q LOSS WILD-TYPE            7          44         42
D78V38, multiclass
              clus
vv             21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CURRENT USER                3                  7
  FORMER USER                 5                 44
  NEVER USED                 15                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V39, continuous
D78V40, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   15  4
  21Q LOSS WILD-TYPE 74 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     15    4
  21Q LOSS WILD-TYPE   74   12
         clus
vv        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ABSENT                15                 74
  PRESENT                4                 12
[1] 2 2
[1] FALSE
D78V41, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  21Q LOSS MUTATED     0    0   5   12    3  1   3    3    0   4  0   5  0   0
  21Q LOSS WILD-TYPE   1    1  25   53   21  3   5    4    9  18  1   3  2   1
                    vv
clus                 TX
  21Q LOSS MUTATED    1
  21Q LOSS WILD-TYPE 13
D78V42, multiclass
      clus
vv     21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 5                 25
  T1B1               12                 53
  T1B2                3                 21
  T2                  1                  3
  T2A                 3                  5
  T2A1                3                  4
  T2A2                0                  9
  T2B                 4                 18
  T3                  0                  1
  T3B                 5                  3
  T4                  0                  2
  TIS                 0                  1
  TX                  1                 13
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  21Q LOSS MUTATED         0        0         0         0        7        12
  21Q LOSS WILD-TYPE       4        2         1         1       24        57
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  21Q LOSS MUTATED           4        2         1          3          0
  21Q LOSS WILD-TYPE        28        1         5          2          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  21Q LOSS MUTATED           5         0          6         0         1
  21Q LOSS WILD-TYPE        22         1         28         3         6
D78V44, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  7                 24
  STAGE IB1                12                 57
  STAGE IB2                 4                 28
  STAGE II                  2                  1
  STAGE IIA                 1                  5
  STAGE IIA1                3                  2
  STAGE IIA2                0                  7
  STAGE IIB                 5                 22
  STAGE III                 0                  1
  STAGE IIIB                6                 28
  STAGE IVA                 0                  3
  STAGE IVB                 1                  6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    41  15
  22Q LOSS WILD-TYPE 142  35
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                56                177 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 35 
$`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-A7CM TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ 
       20.35         9.34         2.73        27.52         1.12        58.88 
TCGA-DG-A2KL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 
       44.94       118.65        12.36         1.32         1.35        14.50 
TCGA-EA-A44S TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2R8 
       12.66         0.36        12.59         1.51         0.59         1.45 
TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EX-A8YF TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LB 
        1.18         0.10         4.73        21.67       137.16        66.81 
TCGA-IR-A3LC TCGA-JW-A5VG TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MY-A913 TCGA-Q1-A5R1 
      117.40        27.42         7.99         0.20         5.49        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EC 
       13.35         3.39        19.59        11.67        12.16        34.52 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y 
       14.07        19.96        53.52        39.78        16.64         4.73 
TCGA-VS-A952 TCGA-VS-A957 
       44.88        42.08 

$`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-A1ML TCGA-C5-A1MN 
       53.16        38.99        35.61         2.43        20.91        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-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
        0.82        17.85        20.42       182.93       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48       147.35        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95        13.61        50.99        45.83         8.35        75.78 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK 
       99.91        23.51         6.12        20.91         4.47        50.76 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.04        87.75        58.88        36.76         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        17.52         8.28         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.74         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.35         1.81        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        15.02        14.99        14.96        13.58        13.48 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R9 
       45.96        26.27         6.64         0.43         0.59         0.13 
TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
       16.08         0.07         4.04         0.03         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        19.79         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-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
        1.97         1.12         9.01        25.41         7.13        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
       14.93         9.44       147.39        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        10.06         5.13         6.71        21.11       195.85 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       30.31        11.28         0.89         0.07         0.30         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-A73O TCGA-Q1-A73P 
        2.96        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI 
        5.88         6.25        10.39         3.88        93.99        61.28 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       10.03        29.03        20.22        32.15        46.03        23.28 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Z TCGA-VS-A954 TCGA-VS-A958 
       11.51        49.55        31.27        23.24        42.58        43.82 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       39.35        38.96        18.05 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            173.29             195.85 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             16.11              15.88 
[1] "0.1 - 173.3 (16.1)" "0.0 - 195.8 (15.9)"
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 T1 T2 T3+T4
  22Q LOSS MUTATED   27 14     3
  22Q LOSS WILD-TYPE 94 36     8
D79V3, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                  27                 94
  T2                  14                 36
  T3+T4                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   28 10
  22Q LOSS WILD-TYPE 83 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     28   10
  22Q LOSS WILD-TYPE   83   37
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               28                 83
  1               10                 37
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   29  2 18
  22Q LOSS WILD-TYPE 62  6 75
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               29                 62
  M1                2                  6
  MX               18                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED               1                               46
  22Q LOSS WILD-TYPE             4                              151
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  22Q LOSS MUTATED                                               1
  22Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  22Q LOSS MUTATED                                     5
  22Q LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  22Q LOSS MUTATED                                           1
  22Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  22Q LOSS MUTATED                                              4
  22Q LOSS WILD-TYPE                                            2
D79V6, multiclass
                                               clus
vv                                              22Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            46
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 4
                                               clus
vv                                              22Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             151
  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"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    10  48
  22Q LOSS WILD-TYPE  20 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   48
  22Q LOSS WILD-TYPE   20  160
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                10                 20
  YES               48                160
[1] 2 2
[1] FALSE
D79V8, continuous
D79V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  2     2
  22Q LOSS WILD-TYPE                                6    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED                           6
  22Q LOSS WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           0    45
  22Q LOSS WILD-TYPE                                         1   124
D79V10, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                6                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   45                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"
D79V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4  32
  22Q LOSS WILD-TYPE  12 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4   32
  22Q LOSS WILD-TYPE   12  117
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               32                117
[1] 2 2
[1] FALSE
D79V12, continuous
D79V13, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   20  6
  22Q LOSS WILD-TYPE 51 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     20    6
  22Q LOSS WILD-TYPE   51   19
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  TUMOR FREE               20                 51
  WITH TUMOR                6                 19
[1] 2 2
[1] FALSE
                    vv
clus                 BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  22Q LOSS MUTATED        9      3       0      3       2            39       2
  22Q LOSS WILD-TYPE     14      2       1      7       5           139      12
D79V14, multiclass
               clus
vv              22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  BRAZIL                       9                 14
  CANADA                       3                  2
  NIGERIA                      0                  1
  RUSSIA                       3                  7
  UKRAINE                      2                  5
  UNITED STATES               39                139
  VIETNAM                      2                 12
[1] 7 2
[1] 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    4 23 27  0  4
  22Q LOSS WILD-TYPE 13 83 70  1 10
D79V15, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  G1                4                 13
  G2               23                 83
  G3               27                 70
  G4                0                  1
  GX                4                 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"
D79V16, continuous
D79V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  22Q LOSS MUTATED                                             5
  22Q LOSS WILD-TYPE                                          26
                    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                                                 1
  22Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  22Q LOSS MUTATED                9                  31
  22Q LOSS WILD-TYPE             43                  81
D79V18, multiclass
                                                 clus
vv                                                22Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 9
  LIFELONG NON-SMOKER                                           31
                                                 clus
vv                                                22Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  43
  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"
D79V19, continuous
D79V20, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  22Q LOSS MUTATED             6       22             4        4
  22Q LOSS WILD-TYPE          13       53             8        8
D79V21, multiclass
               clus
vv              22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COMBINATION                  6                 13
  EXTERNAL                    22                 53
  EXTERNAL BEAM                4                  8
  INTERNAL                     4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V22, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    9  0
  22Q LOSS WILD-TYPE 16  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9    0
  22Q LOSS WILD-TYPE   16    3
                         clus
vv                        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  22Q LOSS MUTATED                    1                1                  11
  22Q LOSS WILD-TYPE                  1                1                  17
                    vv
clus                 REGIONAL SITE
  22Q LOSS MUTATED               3
  22Q LOSS WILD-TYPE            13
D79V23, multiclass
                     clus
vv                    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  DISTANT RECURRENCE                 1                  1
  LOCAL RECURRENCE                   1                  1
  PRIMARY TUMOR FIELD               11                 17
  REGIONAL SITE                      3                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V24, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   12  2
  22Q LOSS WILD-TYPE 22  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     12    2
  22Q LOSS WILD-TYPE   22    1
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CGY               12                 22
  GY                 2                  1
[1] 2 2
[1] FALSE
D79V25, continuous
D79V26, continuous
D79V27, continuous
D79V28, continuous
D79V29, continuous
D79V30, 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                         9                       0
  22Q LOSS WILD-TYPE                      20                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  22Q LOSS MUTATED                         2
  22Q LOSS WILD-TYPE                       5
D79V31, multiclass
                                     clus
vv                                    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            9                 20
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  22Q LOSS MUTATED                                               1
  22Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  22Q LOSS MUTATED                                                2
  22Q LOSS WILD-TYPE                                             14
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  22Q LOSS MUTATED                                                                                  20
  22Q LOSS WILD-TYPE                                                                                48
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  22Q LOSS MUTATED                                                                                             23
  22Q LOSS WILD-TYPE                                                                                           82
D79V32, multiclass
                                                                                              clus
vv                                                                                             22Q 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)                          20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               23
                                                                                              clus
vv                                                                                             22Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V33, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   16 19
  22Q LOSS WILD-TYPE 52 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     16   19
  22Q LOSS WILD-TYPE   52   51
         clus
vv        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ABSENT                16                 52
  PRESENT               19                 51
[1] 2 2
[1] FALSE
D79V34, continuous
D79V35, continuous
D79V36, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    9 23
  22Q LOSS WILD-TYPE 34 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   23
  22Q LOSS WILD-TYPE   34   71
                                          clus
vv                                         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               23                 71
[1] 2 2
[1] FALSE
D79V37, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  22Q LOSS MUTATED              5          11         16
  22Q LOSS WILD-TYPE            5          38         41
D79V38, multiclass
              clus
vv             22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CURRENT USER                5                  5
  FORMER USER                11                 38
  NEVER USED                 16                 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"
D79V39, continuous
D79V40, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   24  2
  22Q LOSS WILD-TYPE 65 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24    2
  22Q LOSS WILD-TYPE   65   14
         clus
vv        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ABSENT                24                 65
  PRESENT                2                 14
[1] 2 2
[1] FALSE
D79V41, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 11 
        TCGA-C5-A1MH         TCGA-C5-A1ML         TCGA-C5-A1MN 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"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 T3 T3B T4 TIS
  22Q LOSS MUTATED     0    0   9   13    5  2   4    2    1   5  0   3  0   1
  22Q LOSS WILD-TYPE   1    1  21   52   19  2   4    5    8  17  1   5  2   0
                    vv
clus                 TX
  22Q LOSS MUTATED    4
  22Q LOSS WILD-TYPE 10
D79V42, multiclass
      clus
vv     22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1A                 0                  1
  T1A1                0                  1
  T1B                 9                 21
  T1B1               13                 52
  T1B2                5                 19
  T2                  2                  2
  T2A                 4                  4
  T2A1                2                  5
  T2A2                1                  8
  T2B                 5                 17
  T3                  0                  1
  T3B                 3                  5
  T4                  0                  2
  TIS                 1                  0
  TX                  4                 10
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V43, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  22Q LOSS MUTATED         1        0         0         0        9        20
  22Q LOSS WILD-TYPE       3        2         1         1       22        49
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  22Q LOSS MUTATED           6        2         4          1          0
  22Q LOSS WILD-TYPE        26        1         2          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  22Q LOSS MUTATED           7         0          6         0         0
  22Q LOSS WILD-TYPE        20         1         28         3         7
D79V44, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  0                  2
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  9                 22
  STAGE IB1                20                 49
  STAGE IB2                 6                 26
  STAGE II                  2                  1
  STAGE IIA                 4                  2
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 7                 20
  STAGE III                 0                  1
  STAGE IIIB                6                 28
  STAGE IVA                 0                  3
  STAGE IVB                 0                  7
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    30  13
  XQ LOSS WILD-TYPE 153  37
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               43               190 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               13                37 
$`XQ LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A1MK TCGA-C5-A1ML 
       23.67        11.44        19.86        30.21         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A3HD TCGA-C5-A7CJ TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7X5 
       40.93        52.01       101.82       147.35        60.69        13.61 
TCGA-C5-A8XK TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3QE 
       99.91        36.76       118.65        16.18        12.36         1.18 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EK-A2PL TCGA-EK-A2RA 
        1.81        12.66        14.89        14.99         0.43        16.08 
TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.36         2.24         0.10         0.10        20.35         7.92 
TCGA-EX-A69M TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A5XV TCGA-IR-A3LK TCGA-JW-A5VL 
        6.12         0.92         0.66         1.97        26.56        15.58 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-MY-A5BF TCGA-UC-A7PI 
        5.13        21.11        30.31         0.89         4.34        61.28 
TCGA-VS-A94Y 
        4.73 

$`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       154.32       134.33        15.48        20.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
       17.19        85.55        94.95         9.34         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35        75.78        23.51        27.52         6.12 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91         4.47         1.12        58.88        50.76        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       40.04        87.75        58.88         2.66       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.83        17.52         8.28         0.76         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.82         0.62        13.05        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       14.50        12.82         0.26         1.48        13.91        15.02 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.96        13.58        13.48         0.36        12.59        45.96 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         6.64         1.51         0.59         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.13         0.07         4.04         0.03         1.18        23.70 
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        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI 
        4.73         1.22        23.84         2.17         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-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12         9.01        25.41         7.13        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        78.71        81.96        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3Q0 
       24.56        21.44        20.48        10.06         6.71       195.85 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
        7.99        11.28         0.07         0.30         0.82         0.20 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 
       13.87         0.03         5.42        29.72         0.07         5.49 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        13.35        15.95         3.39        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         5.88         6.25        10.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB 
       19.59         3.88        11.67        93.99        12.16        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       34.52        29.03        20.22        14.07        19.96        53.52 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        46.03        23.28        11.51        49.55        39.78 
TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
       31.27        16.64        23.24        44.88        42.58        42.08 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-WL-A834 
       43.82        39.35        38.96        18.05 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           147.35            195.85 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            14.89             16.39 
[1] "0.1 - 147.3 (14.9)" "0.0 - 195.8 (16.4)"
[1] "hr=" "1.9"
D80V2, continuous
                   vv
clus                T1 T2 T3+T4
  XQ LOSS MUTATED   25  8     0
  XQ LOSS WILD-TYPE 96 42    11
D80V3, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                 25                96
  T2                  8                42
  T3+T4               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V4, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   23  8
  XQ LOSS WILD-TYPE 88 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     23    8
  XQ LOSS WILD-TYPE   88   39
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              23                88
  1               8                39
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED   13  0 18
  XQ LOSS WILD-TYPE 78  8 75
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              13                78
  M1               0                 8
  MX              18                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED               1                               38
  XQ LOSS WILD-TYPE             4                              159
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  XQ LOSS MUTATED                                               0
  XQ LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  XQ LOSS MUTATED                                     3
  XQ LOSS WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  XQ LOSS MUTATED                                           2
  XQ LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  XQ LOSS MUTATED                                              0
  XQ LOSS WILD-TYPE                                            6
D80V6, multiclass
                                               clus
vv                                              XQ LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              XQ LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            159
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  6
[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     8  36
  XQ LOSS WILD-TYPE  22 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   36
  XQ LOSS WILD-TYPE   22  172
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                8                22
  YES              36               172
[1] 2 2
[1] FALSE
D80V8, continuous
D80V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  1     3
  XQ LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED                           4
  XQ LOSS WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           1    33
  XQ LOSS WILD-TYPE                                         0   136
D80V10, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   3                15
  BLACK OR AFRICAN AMERICAN                               4                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  33               136
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4  31
  XQ LOSS WILD-TYPE  12 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   31
  XQ LOSS WILD-TYPE   12  118
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                12
  NOT HISPANIC OR LATINO              31               118
[1] 2 2
[1] FALSE
D80V12, continuous
D80V13, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   14  6
  XQ LOSS WILD-TYPE 57 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14    6
  XQ LOSS WILD-TYPE   57   19
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  TUMOR FREE              14                57
  WITH TUMOR               6                19
[1] 2 2
[1] FALSE
                   vv
clus                BRAZIL CANADA NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  XQ LOSS MUTATED        1      0       0      3       2            36       2
  XQ LOSS WILD-TYPE     22      5       1      7       5           142      12
D80V14, multiclass
               clus
vv              XQ LOSS MUTATED XQ LOSS WILD-TYPE
  BRAZIL                      1                22
  CANADA                      0                 5
  NIGERIA                     0                 1
  RUSSIA                      3                 7
  UKRAINE                     2                 5
  UNITED STATES              36               142
  VIETNAM                     2                12
[1] 7 2
[1] 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    5 16 21  0  1
  XQ LOSS WILD-TYPE 12 90 76  1 13
D80V15, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  G1               5                12
  G2              16                90
  G3              21                76
  G4               0                 1
  GX               1                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V16, continuous
D80V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  XQ LOSS MUTATED                                             6
  XQ LOSS WILD-TYPE                                          25
                   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                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  XQ LOSS MUTATED                9                  19
  XQ LOSS WILD-TYPE             43                  93
D80V18, multiclass
                                                 clus
vv                                                XQ 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                                                9
  LIFELONG NON-SMOKER                                          19
                                                 clus
vv                                                XQ LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    25
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 43
  LIFELONG NON-SMOKER                                            93
[1] 5 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
D80V20, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  XQ LOSS MUTATED             4        7             4        2
  XQ LOSS WILD-TYPE          15       68             8       10
D80V21, multiclass
               clus
vv              XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COMBINATION                 4                15
  EXTERNAL                    7                68
  EXTERNAL BEAM               4                 8
  INTERNAL                    2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V22, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    5  2
  XQ LOSS WILD-TYPE 20  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      5    2
  XQ LOSS WILD-TYPE   20    1
                         clus
vv                        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                DISTANT RECURRENCE LOCAL RECURRENCE PRIMARY TUMOR FIELD
  XQ LOSS MUTATED                    1                1                   3
  XQ LOSS WILD-TYPE                  1                1                  25
                   vv
clus                REGIONAL SITE
  XQ LOSS MUTATED               2
  XQ LOSS WILD-TYPE            14
D80V23, multiclass
                     clus
vv                    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  DISTANT RECURRENCE                1                 1
  LOCAL RECURRENCE                  1                 1
  PRIMARY TUMOR FIELD               3                25
  REGIONAL SITE                     2                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V24, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3  0
  XQ LOSS WILD-TYPE 31  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE   31    3
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CGY               3                31
  GY                0                 3
[1] 2 2
[1] FALSE
D80V25, continuous
D80V26, continuous
D80V27, continuous
D80V28, continuous
D80V29, continuous
D80V30, 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                       3
  XQ LOSS WILD-TYPE                                   2                      26
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  XQ LOSS MUTATED                         0                       1
  XQ LOSS WILD-TYPE                       1                       6
D80V31, multiclass
                                     clus
vv                                    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               4                 2
  OTHER LOCATION, SPECIFY                           3                26
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  XQ LOSS MUTATED                                               1
  XQ LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  XQ LOSS MUTATED                                                3
  XQ LOSS WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  XQ LOSS MUTATED                                                                                  10
  XQ LOSS WILD-TYPE                                                                                58
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  XQ LOSS MUTATED                                                                                             19
  XQ LOSS WILD-TYPE                                                                                           86
D80V32, 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)                         10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              19
                                                                                              clus
vv                                                                                             XQ LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           58
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V33, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   13 12
  XQ LOSS WILD-TYPE 55 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13   12
  XQ LOSS WILD-TYPE   55   58
         clus
vv        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ABSENT               13                55
  PRESENT              12                58
[1] 2 2
[1] FALSE
D80V34, continuous
D80V35, continuous
D80V36, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   14 15
  XQ LOSS WILD-TYPE 29 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14   15
  XQ LOSS WILD-TYPE   29   79
                                          clus
vv                                         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  14                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              15                79
[1] 2 2
[1] FALSE
D80V37, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  XQ LOSS MUTATED              3           9         12
  XQ LOSS WILD-TYPE            7          40         45
D80V38, multiclass
              clus
vv             XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CURRENT USER               3                 7
  FORMER USER                9                40
  NEVER USED                12                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"
D80V39, continuous
D80V40, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   18  2
  XQ LOSS WILD-TYPE 71 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     18    2
  XQ LOSS WILD-TYPE   71   14
         clus
vv        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ABSENT               18                71
  PRESENT               2                14
[1] 2 2
[1] FALSE
D80V41, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3 T3B T4 TIS
  XQ LOSS MUTATED     0    0   6   12    7  0   1    0    4   3  0   0  0   0
  XQ LOSS WILD-TYPE   1    1  24   53   17  4   7    7    5  19  1   8  2   1
                   vv
clus                TX
  XQ LOSS MUTATED    0
  XQ LOSS WILD-TYPE 14
D80V42, multiclass
      clus
vv     XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1A                0                 1
  T1A1               0                 1
  T1B                6                24
  T1B1              12                53
  T1B2               7                17
  T2                 0                 4
  T2A                1                 7
  T2A1               0                 7
  T2A2               4                 5
  T2B                3                19
  T3                 0                 1
  T3B                0                 8
  T4                 0                 2
  TIS                0                 1
  TX                 0                14
[1] 15  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V43, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  XQ LOSS MUTATED         0        1         0         1        6        11
  XQ LOSS WILD-TYPE       4        1         1         0       25        58
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  XQ LOSS MUTATED           8        0         2          0          2
  XQ LOSS WILD-TYPE        24        3         4          5          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIB STAGE IVA STAGE IVB
  XQ LOSS MUTATED           4         0          7         0         1
  XQ LOSS WILD-TYPE        23         1         27         3         6
D80V44, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1                 1
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                 6                25
  STAGE IB1               11                58
  STAGE IB2                8                24
  STAGE II                 0                 3
  STAGE IIA                2                 4
  STAGE IIA1               0                 5
  STAGE IIA2               2                 5
  STAGE IIB                4                23
  STAGE III                0                 1
  STAGE IIIB               7                27
  STAGE IVA                0                 3
  STAGE IVB                1                 6
[1] 16  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
