[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTCESC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/10005797/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/10013672/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=206, common to both=176
[1]  57 176
[1] "AMP PEAK  1(1P31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           56                           120 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           56                           120 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           92                            84 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           92                            84 
[1] "AMP PEAK  3(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           43                           133 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           43                           133 
[1] "AMP PEAK  4(2Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                           28                           148 
  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                           28                           148 
[1] "AMP PEAK  5(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                           134                             42 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                           134                             42 
[1] "AMP PEAK  6(3Q28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE 
                        134                          42 
  AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE 
                        134                          42 
[1] "AMP PEAK  7(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                         12                         164 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                         12                         164 
[1] "AMP PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            75                            101 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            75                            101 
[1] "AMP PEAK  9(6P21.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE 
                            48                            128 
  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE 
                            48                            128 
[1] "AMP PEAK 10(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                           32                           144 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                           32                           144 
[1] "AMP PEAK 11(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            72                            104 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            72                            104 
[1] "AMP PEAK 12(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                           37                           139 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                           37                           139 
[1] "AMP PEAK 13(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          14                          162 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          14                          162 
[1] "AMP PEAK 14(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            22                            154 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            22                            154 
[1] "AMP PEAK 15(11Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE 
                            31                            145 
  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE 
                            31                            145 
[1] "AMP PEAK 16(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                            39                            137 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                            39                            137 
[1] "AMP PEAK 17(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            43                            133 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            43                            133 
[1] "AMP PEAK 18(16P13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                             35                             141 
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                             35                             141 
[1] "AMP PEAK 19(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          31                          145 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          31                          145 
[1] "AMP PEAK 20(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            46                            130 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            46                            130 
[1] "AMP PEAK 21(19Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE 
                            53                            123 
  AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE 
                            53                            123 
[1] "AMP PEAK 22(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                             76                             100 
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                             76                             100 
[1] "AMP PEAK 23(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE 
                         43                         133 
  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE 
                         43                         133 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            25                            151 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            25                            151 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           19                           157 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           19                           157 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           30                           146 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           30                           146 
[1] "DEL PEAK  4(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                           69                           107 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                           69                           107 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           66                           110 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           66                           110 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           74                           102 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           74                           102 
[1] "DEL PEAK  7(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                           52                           124 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                           52                           124 
[1] "DEL PEAK  8(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           49                           127 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           49                           127 
[1] "DEL PEAK  9(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE 
                           64                           112 
  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE 
                           64                           112 
[1] "DEL PEAK 10(5Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE 
                           47                           129 
  DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE 
                           47                           129 
[1] "DEL PEAK 11(5Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE 
                           47                           129 
  DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE 
                           47                           129 
[1] "DEL PEAK 12(6P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE 
                           23                           153 
  DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE 
                           23                           153 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         61                         115 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         61                         115 
[1] "DEL PEAK 14(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE 
                         40                         136 
  DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE 
                         40                         136 
[1] "DEL PEAK 15(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE 
                           62                           114 
  DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE 
                           62                           114 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             53                             123 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             53                             123 
[1] "DEL PEAK 17(11P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            58                            118 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            58                            118 
[1] "DEL PEAK 18(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE 
                         101                           75 
  DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE 
                         101                           75 
[1] "DEL PEAK 19(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE 
                             61                             115 
  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE 
                             61                             115 
[1] "DEL PEAK 20(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE 
                            67                            109 
  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE 
                            67                            109 
[1] "DEL PEAK 21(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE 
                             27                             149 
  DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE 
                             27                             149 
[1] "DEL PEAK 22(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE 
                            37                            139 
  DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE 
                            37                            139 
[1] "DEL PEAK 23(16Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE 
                            35                            141 
  DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE 
                            35                            141 
[1] "DEL PEAK 24(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE 
                            34                            142 
  DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE 
                            34                            142 
[1] "DEL PEAK 25(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE 
                          58                          118 
  DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE 
                          58                          118 
[1] "DEL PEAK 26(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE 
                            31                            145 
  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE 
                            31                            145 
[1] "DEL PEAK 27(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE 
                            50                            126 
  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE 
                            50                            126 
[1] "DEL PEAK 28(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE 
                            55                            121 
  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE 
                            55                            121 
[1] "DEL PEAK 29(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE 
                             21                             155 
  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE 
                             21                             155 
[1] "DEL PEAK 30(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            23                            153 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            23                            153 
[1] "DEL PEAK 31(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                            33                            143 
  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                            33                            143 
[1] "DEL PEAK 32(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             47                             129 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             47                             129 
[1] "DEL PEAK 33(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE 
                           43                           133 
  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE 
                           43                           133 
[1] "DEL PEAK 34(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE 
                            36                            140 
  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE 
                            36                            140 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                    
 [2] "VITALSTATUS"                                     
 [3] "DAYSTODEATH"                                     
 [4] "DAYSTOLASTFOLLOWUP"                              
 [5] "PRIMARYSITEOFDESEASE"                            
 [6] "NEOPLASM.DISEASESTAGE"                           
 [7] "PATHOLOGY.T.STAGE"                               
 [8] "PATHOLOGY.N.STAGE"                               
 [9] "PATHOLOGY.M.STAGE"                               
[10] "DCCUPLOADDATE"                                   
[11] "GENDER"                                          
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                
[13] "HISTOLOGICALTYPE"                                
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"          
[15] "NUMBERPACKYEARSSMOKED"                           
[16] "NUMBER.OF.LYMPH.NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCHNUMBER"                                     
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASMHISTOLOGICGRADE"                         
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_THERAPY_TYPE"                          
[30] "RADIATION_THERAPY_STATUS"                        
[31] "RADIATION_ADJUVANT_UNITS"                        
[32] "PREGNANCIES_COUNT_TOTAL"                         
[33] "PREGNANCIES_COUNT_STILLBIRTH"                    
[34] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[35] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[36] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_ECTOPIC"                       
[38] "PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[39] "LYMPH_NODE_LOCATION"                             
[40] "LOCATION_OF_POSITIVE_MARGINS"                    
[41] "MENOPAUSE_STATUS"                                
[42] "LYMPHOVASCULAR_INVOLVEMENT"                      
[43] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[44] "LYMPH_NODES_EXAMINED"                            
[45] "KERATINIZATION_SQUAMOUS_CELL"                    
[46] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[47] "HYSTERECTOMY_TYPE"                               
[48] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[49] "HEIGHT_CM_AT_DIAGNOSIS"                          
[50] "FEDPET_OR_CT_RESULTS"                            
[51] "CORPUS_INVOLVEMENT"                              
[52] "CHEMO_CONCURRENT_TYPE"                           
[53] "CERVIX_SUV_RESULTS"                              
[54] "CAUSE_OF_DEATH"                                  
[55] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[56] "AGE_AT_DIAGNOSIS"                                

Input Data has 56 rows and 176 columns.

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

$Table
vv
T1 T2 T3 T4 
97 36  2  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 97

$Class1_nSamples
[1] 39

$Class0_label
[1] "T1"

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


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

Clustering(1) Variable = AMP PEAK  1(1P31.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1P31.3) MUTATED   43 10
  AMP PEAK  1(1P31.3) WILD-TYPE 94 22
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           53                           116 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                           10                            22 
$`AMP PEAK  1(1P31.3) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        57.04        36.56        82.85        31.40        46.32 
TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CH 
       38.99         0.46         2.43       100.14        17.85        25.35 
TCGA-C5-A7CJ TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A7WI 
      101.82        13.61         2.73         2.66       118.65         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A439 
        0.76         1.74         0.62         1.18         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EK-A2PG TCGA-EK-A2R7 
        1.81        13.91         0.69        14.96         0.53         0.59 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A69L 
        1.18         2.24         0.10         0.07         0.03         4.47 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LC 
        1.45         1.58         1.35        20.78        14.93       117.40 
TCGA-IR-A3LL TCGA-JW-A5VK TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-PN-A8MA 
       36.36        20.48        13.87         0.03         0.07         2.96 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-R2-A69V TCGA-UC-A7PF 
        3.45         3.39         5.75        19.59        93.99 

$`AMP PEAK  1(1P31.3) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK 
       23.67        11.44        68.84        18.74       144.16       177.04 
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-A7CK TCGA-C5-A7CL 
       52.01        18.02        20.42       182.93       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A3LQ 
        9.34        87.75        58.88        36.76       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
       16.83        16.18         7.33        12.36         1.32         0.82 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       13.05        14.50         1.35        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       14.89         1.48        14.99        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
       45.96         6.64         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
       23.70         0.10         0.10        20.35         7.92         6.94 
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-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        0.66         1.02         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.97         1.12        25.41        21.67         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81        96.95        78.71        81.96        26.56 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       14.43        16.64        19.33        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A8JM TCGA-MY-A5BD 
        0.10         0.89         0.07         0.82         5.42        29.72 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R 
        4.34         3.72         5.85         3.72         4.80         6.25 
TCGA-RA-A741 TCGA-UC-A7PD 
        3.88        11.67 

  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                         0.03                          0.03 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                       118.65                        182.93 
  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE 
                         4.47                         14.60 
[1] "0.0 - 118.7 (4.5)"  "0.0 - 182.9 (14.6)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            T1 T2+T3+T4
  AMP PEAK  1(1P31.3) MUTATED   27       13
  AMP PEAK  1(1P31.3) WILD-TYPE 70       26
D1V3, multiclass
          clus
vv         AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  T1                                27                            70
  T2+T3+T4                          13                            26
[1] 2 2
[1] FALSE
D1V4, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   23 14
  AMP PEAK  1(1P31.3) WILD-TYPE 64 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     23   14
  AMP PEAK  1(1P31.3) WILD-TYPE   64   26
   clus
vv  AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  0                          23                            64
  1                          14                            26
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  1(1P31.3) MUTATED   24  0 19
  AMP PEAK  1(1P31.3) WILD-TYPE 48  3 46
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  M0                          24                            48
  M1                           0                             3
  MX                          19                            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1P31.3) MUTATED               0                               52
  AMP PEAK  1(1P31.3) WILD-TYPE             2                               92
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  1(1P31.3) MUTATED                                               0
  AMP PEAK  1(1P31.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  1(1P31.3) MUTATED                                     2
  AMP PEAK  1(1P31.3) WILD-TYPE                                  18
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  1(1P31.3) MUTATED                                           0
  AMP PEAK  1(1P31.3) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  1(1P31.3) MUTATED                                              2
  AMP PEAK  1(1P31.3) WILD-TYPE                                            2
D1V6, multiclass
                                               clus
vv                                              AMP PEAK  1(1P31.3) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       52
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              AMP PEAK  1(1P31.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         92
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P31.3) MUTATED     8  48
  AMP PEAK  1(1P31.3) WILD-TYPE  19 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      8   48
  AMP PEAK  1(1P31.3) WILD-TYPE   19  101
     clus
vv    AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  NO                            8                            19
  YES                          48                           101
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P31.3) MUTATED                                  1     5
  AMP PEAK  1(1P31.3) WILD-TYPE                                6    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P31.3) MUTATED                           7
  AMP PEAK  1(1P31.3) WILD-TYPE                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  1(1P31.3) MUTATED                                           0    42
  AMP PEAK  1(1P31.3) WILD-TYPE                                         1    88
D1V10, multiclass
                                           clus
vv                                          AMP PEAK  1(1P31.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              42
                                           clus
vv                                          AMP PEAK  1(1P31.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                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"
D1V11, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED    1 44
  AMP PEAK  1(1P31.3) WILD-TYPE 10 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      1   44
  AMP PEAK  1(1P31.3) WILD-TYPE   10   83
                        clus
vv                       AMP PEAK  1(1P31.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       AMP PEAK  1(1P31.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                            83
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   11  7
  AMP PEAK  1(1P31.3) WILD-TYPE 37 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     11    7
  AMP PEAK  1(1P31.3) WILD-TYPE   37   12
            clus
vv           AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  TUMOR FREE                          11                            37
  WITH TUMOR                           7                            12
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  1(1P31.3) MUTATED         1      5       2            44       4
  AMP PEAK  1(1P31.3) WILD-TYPE       0      5       4           103       8
D1V14, multiclass
               clus
vv              AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  NIGERIA                                 1                             0
  RUSSIA                                  5                             5
  UKRAINE                                 2                             4
  UNITED STATES                          44                           103
  VIETNAM                                 4                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  1(1P31.3) MUTATED    2 28 24  0  2
  AMP PEAK  1(1P31.3) WILD-TYPE 12 55 48  1  3
D1V15, multiclass
    clus
vv   AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  G1                           2                            12
  G2                          28                            55
  G3                          24                            48
  G4                           0                             1
  GX                           2                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V16, continuous
D1V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  1(1P31.3) MUTATED                                             4
  AMP PEAK  1(1P31.3) WILD-TYPE                                          17
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  1(1P31.3) MUTATED                                        4
  AMP PEAK  1(1P31.3) WILD-TYPE                                      4
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  1(1P31.3) MUTATED                                                 0
  AMP PEAK  1(1P31.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  1(1P31.3) MUTATED               10                  27
  AMP PEAK  1(1P31.3) WILD-TYPE             26                  56
D1V18, multiclass
                                                 clus
vv                                                AMP PEAK  1(1P31.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           10
  LIFELONG NON-SMOKER                                                      27
                                                 clus
vv                                                AMP PEAK  1(1P31.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             26
  LIFELONG NON-SMOKER                                                        56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  1(1P31.3) MUTATED             6       11             2        0
  AMP PEAK  1(1P31.3) WILD-TYPE          11       26             9        5
D1V20, multiclass
               clus
vv              AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  COMBINATION                             6                            11
  EXTERNAL                               11                            26
  EXTERNAL BEAM                           2                             9
  INTERNAL                                0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V21, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED    1  1
  AMP PEAK  1(1P31.3) WILD-TYPE 10  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED      1    1
  AMP PEAK  1(1P31.3) WILD-TYPE   10    2
     clus
vv    AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  CGY                           1                            10
  GY                            1                             2
[1] 2 2
[1] FALSE
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
D1V26, continuous
D1V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  1(1P31.3) MUTATED                                     1
  AMP PEAK  1(1P31.3) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  1(1P31.3) MUTATED                                     0
  AMP PEAK  1(1P31.3) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  1(1P31.3) MUTATED                         4                       0
  AMP PEAK  1(1P31.3) WILD-TYPE                       5                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  1(1P31.3) MUTATED                         1
  AMP PEAK  1(1P31.3) WILD-TYPE                       4
D1V28, multiclass
                                     clus
vv                                    AMP PEAK  1(1P31.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       4
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    AMP PEAK  1(1P31.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                         5
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  AMP PEAK  1(1P31.3) MUTATED                                               0
  AMP PEAK  1(1P31.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  1(1P31.3) MUTATED                                                2
  AMP PEAK  1(1P31.3) WILD-TYPE                                              8
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  1(1P31.3) MUTATED                                                                                  22
  AMP PEAK  1(1P31.3) WILD-TYPE                                                                                32
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  1(1P31.3) MUTATED                                                                                             23
  AMP PEAK  1(1P31.3) WILD-TYPE                                                                                           54
D1V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  1(1P31.3) 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)                                     22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          23
                                                                                              clus
vv                                                                                             AMP PEAK  1(1P31.3) 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)                                       32
  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"
D1V30, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   15 20
  AMP PEAK  1(1P31.3) WILD-TYPE 39 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     15   20
  AMP PEAK  1(1P31.3) WILD-TYPE   39   39
         clus
vv        AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  ABSENT                           15                            39
  PRESENT                          20                            39
[1] 2 2
[1] FALSE
D1V31, continuous
D1V32, continuous
D1V33, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   13 26
  AMP PEAK  1(1P31.3) WILD-TYPE 22 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     13   26
  AMP PEAK  1(1P31.3) WILD-TYPE   22   55
                                          clus
vv                                         AMP PEAK  1(1P31.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          26
                                          clus
vv                                         AMP PEAK  1(1P31.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            55
[1] 2 2
[1] FALSE
D1V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  1(1P31.3) MUTATED       0                   37                   0
  AMP PEAK  1(1P31.3) WILD-TYPE     3                   76                   5
D1V35, multiclass
                      clus
vv                     AMP PEAK  1(1P31.3) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          37
  SIMPLE HYSTERECTOMY                            0
                      clus
vv                     AMP PEAK  1(1P31.3) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            76
  SIMPLE HYSTERECTOMY                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  1(1P31.3) MUTATED              2           8         12
  AMP PEAK  1(1P31.3) WILD-TYPE            6          32         28
D1V36, multiclass
              clus
vv             AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  CURRENT USER                           2                             6
  FORMER USER                            8                            32
  NEVER USED                            12                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V37, continuous
D1V38, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P31.3) MUTATED   19  5
  AMP PEAK  1(1P31.3) WILD-TYPE 54  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P31.3) MUTATED     19    5
  AMP PEAK  1(1P31.3) WILD-TYPE   54    9
         clus
vv        AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  ABSENT                           19                            54
  PRESENT                           5                             9
[1] 2 2
[1] FALSE
D1V39, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK  1(1P31.3) MUTATED     0    1   6   15    5  1   3    3    1   5   0
  AMP PEAK  1(1P31.3) WILD-TYPE   2    0  16   36   16  2   3    3    7   8   2
                               vv
clus                            T4 TX
  AMP PEAK  1(1P31.3) MUTATED    0  4
  AMP PEAK  1(1P31.3) WILD-TYPE  1  3
D1V40, multiclass
      clus
vv     AMP PEAK  1(1P31.3) MUTATED AMP PEAK  1(1P31.3) WILD-TYPE
  T1A                            0                             2
  T1A1                           1                             0
  T1B                            6                            16
  T1B1                          15                            36
  T1B2                           5                            16
  T2                             1                             2
  T2A                            3                             3
  T2A1                           3                             3
  T2A2                           1                             7
  T2B                            5                             8
  T3B                            0                             2
  T4                             0                             1
  TX                             4                             3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V41, continuous

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   70 17
  AMP PEAK  2(1Q21.3) WILD-TYPE 67 15
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           87                            82 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           17                            15 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        57.04        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF 
      173.29        82.85         5.46        31.40        46.32        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         0.46         2.43         3.58        44.22 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       78.35       100.14        17.85        25.35       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       15.48        94.95        13.61         2.73        87.75        58.88 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
        2.66       117.99        22.98         7.33         8.28         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A439 
        1.74         1.32         0.82         0.62         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.81        13.91         0.69        14.99        14.96        13.58 
TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
       12.59         0.53         0.59         1.18        23.70         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         4.47 
TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A40J TCGA-HG-A2PA 
        6.12        23.84         2.17         1.45         1.35        25.41 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
       20.78        14.93         4.11       117.40        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A5U3 
       36.36        19.33        20.48         5.13         0.10         0.82 
TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DW 
       13.87         0.07         2.96         3.45         5.85         5.75 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF 
        6.25        19.59        93.99 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 
       23.67        11.44        68.84        19.86        67.46        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       35.01        57.73        40.93        73.18        73.45        83.05 
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-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 
        9.67        73.41        17.19        85.55        60.69         9.34 
TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3QD 
       36.76       118.65        16.83        16.18        12.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.18        14.50         1.35        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RB 
       14.89         1.48        13.48        45.96         6.64         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 
        4.04         0.03         0.36         0.07         0.10        20.35 
TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
        7.92         1.22         0.92         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-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK 
       21.67       147.39       137.16        66.81        96.95        26.56 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A4AX 
       14.43        16.64        15.58        10.06         0.89         0.07 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A6DT 
        0.03         5.42        29.72         4.34         3.72         3.39 
TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-RA-A741 TCGA-UC-A7PD 
        3.72         4.80         3.88        11.67 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.03                          0.03 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       177.04                        182.93 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        13.91                         12.74 
[1] "0.0 - 177.0 (13.9)" "0.0 - 182.9 (12.7)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            T1 T2+T3+T4
  AMP PEAK  2(1Q21.3) MUTATED   44       24
  AMP PEAK  2(1Q21.3) WILD-TYPE 53       15
D2V3, multiclass
          clus
vv         AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                                44                            53
  T2+T3+T4                          24                            15
[1] 2 2
[1] FALSE
D2V4, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   41 24
  AMP PEAK  2(1Q21.3) WILD-TYPE 46 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     41   24
  AMP PEAK  2(1Q21.3) WILD-TYPE   46   16
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                          41                            46
  1                          24                            16
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  2(1Q21.3) MUTATED   40  3 30
  AMP PEAK  2(1Q21.3) WILD-TYPE 32  0 35
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                          40                            32
  M1                           3                             0
  MX                          30                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED               1                               78
  AMP PEAK  2(1Q21.3) WILD-TYPE             1                               66
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                               1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                                    10
  AMP PEAK  2(1Q21.3) WILD-TYPE                                  10
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  2(1Q21.3) MUTATED                                           0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                              2
  AMP PEAK  2(1Q21.3) WILD-TYPE                                            2
D2V6, multiclass
                                               clus
vv                                              AMP PEAK  2(1Q21.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       78
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              AMP PEAK  2(1Q21.3) WILD-TYPE
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         66
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   16 76
  AMP PEAK  2(1Q21.3) WILD-TYPE 11 73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     16   76
  AMP PEAK  2(1Q21.3) WILD-TYPE   11   73
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           16                            11
  YES                          76                            73
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q21.3) MUTATED                                  1    10
  AMP PEAK  2(1Q21.3) WILD-TYPE                                6     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1Q21.3) MUTATED                          13
  AMP PEAK  2(1Q21.3) WILD-TYPE                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           0    66
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         1    64
D2V10, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                              10
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              66
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED    3 67
  AMP PEAK  2(1Q21.3) WILD-TYPE  8 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      3   67
  AMP PEAK  2(1Q21.3) WILD-TYPE    8   60
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          67
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            60
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   25 11
  AMP PEAK  2(1Q21.3) WILD-TYPE 23  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     25   11
  AMP PEAK  2(1Q21.3) WILD-TYPE   23    8
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  TUMOR FREE                          25                            23
  WITH TUMOR                          11                             8
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  2(1Q21.3) MUTATED         1      6       2            75       8
  AMP PEAK  2(1Q21.3) WILD-TYPE       0      4       4            72       4
D2V14, multiclass
               clus
vv              AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NIGERIA                                 1                             0
  RUSSIA                                  6                             4
  UKRAINE                                 2                             4
  UNITED STATES                          75                            72
  VIETNAM                                 8                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  2(1Q21.3) MUTATED    5 44 40  1  2
  AMP PEAK  2(1Q21.3) WILD-TYPE  9 39 32  0  3
D2V15, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  G1                           5                             9
  G2                          44                            39
  G3                          40                            32
  G4                           1                             0
  GX                           2                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V16, continuous
D2V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  2(1Q21.3) MUTATED                                             9
  AMP PEAK  2(1Q21.3) WILD-TYPE                                          12
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  2(1Q21.3) MUTATED                                        4
  AMP PEAK  2(1Q21.3) WILD-TYPE                                      4
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  2(1Q21.3) MUTATED                                                 1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  2(1Q21.3) MUTATED               19                  44
  AMP PEAK  2(1Q21.3) WILD-TYPE             17                  39
D2V18, multiclass
                                                 clus
vv                                                AMP PEAK  2(1Q21.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           19
  LIFELONG NON-SMOKER                                                      44
                                                 clus
vv                                                AMP PEAK  2(1Q21.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             17
  LIFELONG NON-SMOKER                                                        39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  2(1Q21.3) MUTATED            13       20             3        1
  AMP PEAK  2(1Q21.3) WILD-TYPE           4       17             8        4
D2V20, multiclass
               clus
vv              AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  COMBINATION                            13                             4
  EXTERNAL                               20                            17
  EXTERNAL BEAM                           3                             8
  INTERNAL                                1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V21, binary
                               cls
clus                            0 1
  AMP PEAK  2(1Q21.3) MUTATED   4 2
  AMP PEAK  2(1Q21.3) WILD-TYPE 7 1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      4    2
  AMP PEAK  2(1Q21.3) WILD-TYPE    7    1
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  CGY                           4                             7
  GY                            2                             1
[1] 2 2
[1] FALSE
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
D2V26, continuous
D2V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  2(1Q21.3) MUTATED                                     1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  2(1Q21.3) MUTATED                                     1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  2(1Q21.3) MUTATED                         6                       0
  AMP PEAK  2(1Q21.3) WILD-TYPE                       3                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  2(1Q21.3) MUTATED                         3
  AMP PEAK  2(1Q21.3) WILD-TYPE                       2
D2V28, multiclass
                                     clus
vv                                    AMP PEAK  2(1Q21.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                       6
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    AMP PEAK  2(1Q21.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                         3
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  AMP PEAK  2(1Q21.3) MUTATED                                               0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  2(1Q21.3) MUTATED                                                6
  AMP PEAK  2(1Q21.3) WILD-TYPE                                              4
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  2(1Q21.3) MUTATED                                                                                  29
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                                25
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  2(1Q21.3) MUTATED                                                                                             40
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                                           37
D2V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  2(1Q21.3) 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)                                     29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          40
                                                                                              clus
vv                                                                                             AMP PEAK  2(1Q21.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V30, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   28 30
  AMP PEAK  2(1Q21.3) WILD-TYPE 26 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     28   30
  AMP PEAK  2(1Q21.3) WILD-TYPE   26   29
         clus
vv        AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ABSENT                           28                            26
  PRESENT                          30                            29
[1] 2 2
[1] FALSE
D2V31, continuous
D2V32, continuous
D2V33, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   17 41
  AMP PEAK  2(1Q21.3) WILD-TYPE 18 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     17   41
  AMP PEAK  2(1Q21.3) WILD-TYPE   18   40
                                          clus
vv                                         AMP PEAK  2(1Q21.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          41
                                          clus
vv                                         AMP PEAK  2(1Q21.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            40
[1] 2 2
[1] FALSE
D2V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  2(1Q21.3) MUTATED       1                   57                   1
  AMP PEAK  2(1Q21.3) WILD-TYPE     2                   56                   4
D2V35, multiclass
                      clus
vv                     AMP PEAK  2(1Q21.3) MUTATED
  OTHER                                          1
  RADICAL HYSTERECTOMY                          57
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     AMP PEAK  2(1Q21.3) WILD-TYPE
  OTHER                                            2
  RADICAL HYSTERECTOMY                            56
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  2(1Q21.3) MUTATED              4          18         20
  AMP PEAK  2(1Q21.3) WILD-TYPE            4          22         20
D2V36, multiclass
              clus
vv             AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  CURRENT USER                           4                             4
  FORMER USER                           18                            22
  NEVER USED                            20                            20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V37, continuous
D2V38, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   36  8
  AMP PEAK  2(1Q21.3) WILD-TYPE 37  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     36    8
  AMP PEAK  2(1Q21.3) WILD-TYPE   37    6
         clus
vv        AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ABSENT                           36                            37
  PRESENT                           8                             6
[1] 2 2
[1] FALSE
D2V39, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK  2(1Q21.3) MUTATED     1    0   8   26    9  2   5    6    1   9   1
  AMP PEAK  2(1Q21.3) WILD-TYPE   1    1  14   25   12  1   1    0    7   4   1
                               vv
clus                            T4 TX
  AMP PEAK  2(1Q21.3) MUTATED    0  6
  AMP PEAK  2(1Q21.3) WILD-TYPE  1  1
D2V40, multiclass
      clus
vv     AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1A                            1                             1
  T1A1                           0                             1
  T1B                            8                            14
  T1B1                          26                            25
  T1B2                           9                            12
  T2                             2                             1
  T2A                            5                             1
  T2A1                           6                             0
  T2A2                           1                             7
  T2B                            9                             4
  T3B                            1                             1
  T4                             0                             1
  TX                             6                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V41, continuous

Clustering(3) Variable = AMP PEAK  3(2P24.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(2P24.3) MUTATED    35   7
  AMP PEAK  3(2P24.3) WILD-TYPE 102  25
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           42                           127 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                            7                            25 
$`AMP PEAK  3(2P24.3) MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI 
       57.04        23.67         5.46        31.40        57.73        35.61 
TCGA-C5-A1MJ TCGA-C5-A2LT TCGA-C5-A2M2 TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
        0.46        73.18         0.82        60.69         9.34        13.61 
TCGA-C5-A7X8 TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 
        2.73        22.98         7.33         1.32         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2GZ 
        1.81        12.66        14.89        13.91        14.96        12.59 
TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.53         1.18         2.24         0.10         7.92         6.94 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A40J TCGA-IR-A3LA TCGA-IR-A3LC 
       23.84         0.92         0.66         1.35       137.16       117.40 
TCGA-JW-A5VJ TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.33         3.72         3.45         5.85        11.67        93.99 

$`AMP PEAK  3(2P24.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        11.44        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      177.04       173.29        82.85        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MN 
       30.21        35.01        53.16        38.99         2.43        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        3.58        44.22        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       25.35       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       17.19        85.55        94.95        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-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        0.76        12.36         1.74         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.18        14.50         1.35        12.82         0.26         1.48 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP 
        0.69        14.99        13.58        13.48        45.96         6.64 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        0.59         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A449 
        0.10         0.07         0.10         0.03        20.35        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI 
        4.47         6.12         1.22         2.17         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-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-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        14.43        16.64        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
        5.13         0.10         0.89         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 
        3.88 

  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                       137.16                        182.93 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                       10.505                        14.500 
[1] "0.1 - 137.2 (10.5)" "0.0 - 182.9 (14.5)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            T1 T2+T3+T4
  AMP PEAK  3(2P24.3) MUTATED   22        9
  AMP PEAK  3(2P24.3) WILD-TYPE 75       30
D3V3, multiclass
          clus
vv         AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  T1                                22                            75
  T2+T3+T4                           9                            30
[1] 2 2
[1] FALSE
D3V4, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   22  7
  AMP PEAK  3(2P24.3) WILD-TYPE 65 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     22    7
  AMP PEAK  3(2P24.3) WILD-TYPE   65   33
   clus
vv  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  0                          22                            65
  1                           7                            33
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  3(2P24.3) MUTATED   20  0 11
  AMP PEAK  3(2P24.3) WILD-TYPE 52  3 54
D3V5, multiclass
    clus
vv   AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  M0                          20                            52
  M1                           0                             3
  MX                          11                            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(2P24.3) MUTATED               0                               33
  AMP PEAK  3(2P24.3) WILD-TYPE             2                              111
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  3(2P24.3) MUTATED                                               0
  AMP PEAK  3(2P24.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  3(2P24.3) MUTATED                                     6
  AMP PEAK  3(2P24.3) WILD-TYPE                                  14
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  3(2P24.3) MUTATED                                           2
  AMP PEAK  3(2P24.3) WILD-TYPE                                         0
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  3(2P24.3) MUTATED                                              2
  AMP PEAK  3(2P24.3) WILD-TYPE                                            2
D3V6, multiclass
                                               clus
vv                                              AMP PEAK  3(2P24.3) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       33
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            2
                                               clus
vv                                              AMP PEAK  3(2P24.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        111
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED     5  38
  AMP PEAK  3(2P24.3) WILD-TYPE  22 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      5   38
  AMP PEAK  3(2P24.3) WILD-TYPE   22  111
     clus
vv    AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  NO                            5                            22
  YES                          38                           111
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(2P24.3) MUTATED                                  2     2
  AMP PEAK  3(2P24.3) WILD-TYPE                                5    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(2P24.3) MUTATED                           3
  AMP PEAK  3(2P24.3) WILD-TYPE                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(2P24.3) MUTATED                                           1    33
  AMP PEAK  3(2P24.3) WILD-TYPE                                         0    97
D3V10, multiclass
                                           clus
vv                                          AMP PEAK  3(2P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              33
                                           clus
vv                                          AMP PEAK  3(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                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"
D3V11, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED    1 30
  AMP PEAK  3(2P24.3) WILD-TYPE 10 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      1   30
  AMP PEAK  3(2P24.3) WILD-TYPE   10   97
                        clus
vv                       AMP PEAK  3(2P24.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          30
                        clus
vv                       AMP PEAK  3(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                            97
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   11  5
  AMP PEAK  3(2P24.3) WILD-TYPE 37 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     11    5
  AMP PEAK  3(2P24.3) WILD-TYPE   37   14
            clus
vv           AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  TUMOR FREE                          11                            37
  WITH TUMOR                           5                            14
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  3(2P24.3) MUTATED         0      3       3            35       2
  AMP PEAK  3(2P24.3) WILD-TYPE       1      7       3           112      10
D3V14, multiclass
               clus
vv              AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  3                             7
  UKRAINE                                 3                             3
  UNITED STATES                          35                           112
  VIETNAM                                 2                            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  3(2P24.3) MUTATED    2 20 21  0  0
  AMP PEAK  3(2P24.3) WILD-TYPE 12 63 51  1  5
D3V15, multiclass
    clus
vv   AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  G1                           2                            12
  G2                          20                            63
  G3                          21                            51
  G4                           0                             1
  GX                           0                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V16, continuous
D3V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  3(2P24.3) MUTATED                                             3
  AMP PEAK  3(2P24.3) WILD-TYPE                                          18
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  3(2P24.3) MUTATED                                        1
  AMP PEAK  3(2P24.3) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  3(2P24.3) MUTATED                                                 0
  AMP PEAK  3(2P24.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  3(2P24.3) MUTATED                9                  22
  AMP PEAK  3(2P24.3) WILD-TYPE             27                  61
D3V18, multiclass
                                                 clus
vv                                                AMP PEAK  3(2P24.3) 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                                                      22
                                                 clus
vv                                                AMP PEAK  3(2P24.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             27
  LIFELONG NON-SMOKER                                                        61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  3(2P24.3) MUTATED             3       12             2        2
  AMP PEAK  3(2P24.3) WILD-TYPE          14       25             9        3
D3V20, multiclass
               clus
vv              AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  COMBINATION                             3                            14
  EXTERNAL                               12                            25
  EXTERNAL BEAM                           2                             9
  INTERNAL                                2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V21, binary
                               cls
clus                            0 1
  AMP PEAK  3(2P24.3) MUTATED   2 0
  AMP PEAK  3(2P24.3) WILD-TYPE 9 3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      2    0
  AMP PEAK  3(2P24.3) WILD-TYPE    9    3
     clus
vv    AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  CGY                           2                             9
  GY                            0                             3
[1] 2 2
[1] FALSE
D3V22, continuous
D3V23, continuous
D3V24, continuous
D3V25, continuous
D3V26, continuous
D3V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  3(2P24.3) MUTATED                                     0
  AMP PEAK  3(2P24.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  3(2P24.3) MUTATED                                     1
  AMP PEAK  3(2P24.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  3(2P24.3) MUTATED                         2                       0
  AMP PEAK  3(2P24.3) WILD-TYPE                       7                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  3(2P24.3) MUTATED                         0
  AMP PEAK  3(2P24.3) WILD-TYPE                       5
D3V28, multiclass
                                     clus
vv                                    AMP PEAK  3(2P24.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                       2
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    AMP PEAK  3(2P24.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                         7
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  AMP PEAK  3(2P24.3) MUTATED                                               0
  AMP PEAK  3(2P24.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  3(2P24.3) MUTATED                                                3
  AMP PEAK  3(2P24.3) WILD-TYPE                                              7
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  3(2P24.3) MUTATED                                                                                  12
  AMP PEAK  3(2P24.3) WILD-TYPE                                                                                42
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  3(2P24.3) MUTATED                                                                                             19
  AMP PEAK  3(2P24.3) WILD-TYPE                                                                                           58
D3V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  3(2P24.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          19
                                                                                              clus
vv                                                                                             AMP PEAK  3(2P24.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V30, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   14 15
  AMP PEAK  3(2P24.3) WILD-TYPE 40 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     14   15
  AMP PEAK  3(2P24.3) WILD-TYPE   40   44
         clus
vv        AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  ABSENT                           14                            40
  PRESENT                          15                            44
[1] 2 2
[1] FALSE
D3V31, continuous
D3V32, continuous
D3V33, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED    6 19
  AMP PEAK  3(2P24.3) WILD-TYPE 29 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      6   19
  AMP PEAK  3(2P24.3) WILD-TYPE   29   62
                                          clus
vv                                         AMP PEAK  3(2P24.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          19
                                          clus
vv                                         AMP PEAK  3(2P24.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            62
[1] 2 2
[1] FALSE
D3V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  3(2P24.3) MUTATED       0                   28                   1
  AMP PEAK  3(2P24.3) WILD-TYPE     3                   85                   4
D3V35, multiclass
                      clus
vv                     AMP PEAK  3(2P24.3) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          28
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     AMP PEAK  3(2P24.3) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            85
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  3(2P24.3) MUTATED              5          13          9
  AMP PEAK  3(2P24.3) WILD-TYPE            3          27         31
D3V36, multiclass
              clus
vv             AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  CURRENT USER                           5                             3
  FORMER USER                           13                            27
  NEVER USED                             9                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V37, continuous
D3V38, binary
                               cls
clus                             0  1
  AMP PEAK  3(2P24.3) MUTATED   17  4
  AMP PEAK  3(2P24.3) WILD-TYPE 56 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     17    4
  AMP PEAK  3(2P24.3) WILD-TYPE   56   10
         clus
vv        AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  ABSENT                           17                            56
  PRESENT                           4                            10
[1] 2 2
[1] FALSE
D3V39, continuous
[1] "Remove cluster labels:"      "AMP PEAK  3(2P24.3) MUTATED"
clus
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                            1                             8 
                   TCGA-C5-A1MH                    TCGA-C5-A1MN 
"AMP PEAK  3(2P24.3) WILD-TYPE" "AMP PEAK  3(2P24.3) WILD-TYPE" 
                   TCGA-C5-A1MP                    TCGA-EK-A2RO 
"AMP PEAK  3(2P24.3) WILD-TYPE" "AMP PEAK  3(2P24.3) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-JW-A852 
"AMP PEAK  3(2P24.3) WILD-TYPE" "AMP PEAK  3(2P24.3) WILD-TYPE" 
                   TCGA-MU-A51Y                    TCGA-MU-A8JM 
"AMP PEAK  3(2P24.3) WILD-TYPE" "AMP PEAK  3(2P24.3) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK  3(2P24.3) MUTATED     0    0   2   17    3  0   2    4    1   1   1
  AMP PEAK  3(2P24.3) WILD-TYPE   2    1  20   34   18  3   4    2    7  12   1
                               vv
clus                            T4 TX
  AMP PEAK  3(2P24.3) MUTATED    0  2
  AMP PEAK  3(2P24.3) WILD-TYPE  1  5
D3V40, multiclass
      clus
vv     AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  T1A                            0                             2
  T1A1                           0                             1
  T1B                            2                            20
  T1B1                          17                            34
  T1B2                           3                            18
  T2                             0                             3
  T2A                            2                             4
  T2A1                           4                             2
  T2A2                           1                             7
  T2B                            1                            12
  T3B                            1                             1
  T4                             0                             1
  TX                             2                             5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V41, continuous

Clustering(4) Variable = AMP PEAK  4(2Q32.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2Q32.3) MUTATED    18   7
  AMP PEAK  4(2Q32.3) WILD-TYPE 119  25
  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                           25                           144 
  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                            7                            25 
$`AMP PEAK  4(2Q32.3) MUTATED`
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LY 
       57.04        11.44        31.40        35.61         0.46        78.35 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CK TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-DS-A7WI 
        0.82        52.01       134.33        60.69         2.73         8.28 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.50         1.81        14.96        13.58        12.59        45.96 
TCGA-EK-A2RM TCGA-FU-A3NI TCGA-FU-A40J TCGA-JW-A5VL TCGA-LP-A4AX TCGA-UC-A7PD 
        2.24         1.45         1.35        15.58         0.07        11.67 
TCGA-UC-A7PF 
       93.99 

$`AMP PEAK  4(2Q32.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        23.67        68.84        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-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-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        2.43        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       83.05       100.14        38.43        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      182.93        25.35       101.82        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL 
       17.19        85.55        94.95         9.34        13.61        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18         7.33         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
        1.35         1.35        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EK-A2IP 
        1.48        13.91         0.69        14.99        13.48         6.64 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.53         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.18        23.70         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        1.02         1.58         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       19.33        20.48        10.06         5.13         0.10         0.89 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 

  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                       134.33                        182.93 
  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                       13.580                        13.545 
[1] "0.1 - 134.3 (13.6)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.7"
D4V2, continuous
                               vv
clus                            T1 T2+T3+T4
  AMP PEAK  4(2Q32.3) MUTATED   13        4
  AMP PEAK  4(2Q32.3) WILD-TYPE 84       35
D4V3, multiclass
          clus
vv         AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  T1                                13                            84
  T2+T3+T4                           4                            35
[1] 2 2
[1] FALSE
D4V4, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q32.3) MUTATED    7  8
  AMP PEAK  4(2Q32.3) WILD-TYPE 80 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q32.3) MUTATED      7    8
  AMP PEAK  4(2Q32.3) WILD-TYPE   80   32
   clus
vv  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  0                           7                            80
  1                           8                            32
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  4(2Q32.3) MUTATED   11  0  6
  AMP PEAK  4(2Q32.3) WILD-TYPE 61  3 59
D4V5, multiclass
    clus
vv   AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  M0                          11                            61
  M1                           0                             3
  MX                           6                            59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(2Q32.3) MUTATED               0                               23
  AMP PEAK  4(2Q32.3) WILD-TYPE             2                              121
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  4(2Q32.3) MUTATED                                               0
  AMP PEAK  4(2Q32.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  4(2Q32.3) MUTATED                                     4
  AMP PEAK  4(2Q32.3) WILD-TYPE                                  16
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  4(2Q32.3) MUTATED                                           0
  AMP PEAK  4(2Q32.3) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  4(2Q32.3) MUTATED                                              1
  AMP PEAK  4(2Q32.3) WILD-TYPE                                            3
D4V6, multiclass
                                               clus
vv                                              AMP PEAK  4(2Q32.3) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       23
  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                                              AMP PEAK  4(2Q32.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        121
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q32.3) MUTATED     4  24
  AMP PEAK  4(2Q32.3) WILD-TYPE  23 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q32.3) MUTATED      4   24
  AMP PEAK  4(2Q32.3) WILD-TYPE   23  125
     clus
vv    AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  NO                            4                            23
  YES                          24                           125
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(2Q32.3) MUTATED                                  2     4
  AMP PEAK  4(2Q32.3) WILD-TYPE                                5    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(2Q32.3) MUTATED                           2
  AMP PEAK  4(2Q32.3) WILD-TYPE                        16
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(2Q32.3) MUTATED                                           0    19
  AMP PEAK  4(2Q32.3) WILD-TYPE                                         1   111
D4V10, multiclass
                                           clus
vv                                          AMP PEAK  4(2Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              19
                                           clus
vv                                          AMP PEAK  4(2Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               111
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q32.3) MUTATED     2  18
  AMP PEAK  4(2Q32.3) WILD-TYPE   9 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q32.3) MUTATED      2   18
  AMP PEAK  4(2Q32.3) WILD-TYPE    9  109
                        clus
vv                       AMP PEAK  4(2Q32.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       AMP PEAK  4(2Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           109
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q32.3) MUTATED    7  5
  AMP PEAK  4(2Q32.3) WILD-TYPE 41 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q32.3) MUTATED      7    5
  AMP PEAK  4(2Q32.3) WILD-TYPE   41   14
            clus
vv           AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  TUMOR FREE                           7                            41
  WITH TUMOR                           5                            14
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  4(2Q32.3) MUTATED         0      0       1            23       4
  AMP PEAK  4(2Q32.3) WILD-TYPE       1     10       5           124       8
D4V14, multiclass
               clus
vv              AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  0                            10
  UKRAINE                                 1                             5
  UNITED STATES                          23                           124
  VIETNAM                                 4                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK  4(2Q32.3) MUTATED    1 16 11  0  0
  AMP PEAK  4(2Q32.3) WILD-TYPE 13 67 61  1  5
D4V15, multiclass
    clus
vv   AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  G1                           1                            13
  G2                          16                            67
  G3                          11                            61
  G4                           0                             1
  GX                           0                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V16, continuous
[1] "Remove cluster labels:"      "AMP PEAK  4(2Q32.3) MUTATED"
clus
  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                            2                            23 
                   TCGA-BI-A0VR                    TCGA-C5-A1BJ 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-C5-A1BL                    TCGA-C5-A1BQ 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-C5-A1ME                    TCGA-C5-A1MF 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-C5-A1MH                    TCGA-C5-A7CM 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-C5-A7CO                    TCGA-DS-A3LQ 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-EX-A69M                    TCGA-FU-A2QG 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-FU-A3TX                    TCGA-FU-A3WB 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-HM-A4S6 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-IR-A3L7                    TCGA-IR-A3LB 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-IR-A3LH                    TCGA-MU-A5YI 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-MU-A8JM                    TCGA-Q1-A6DW 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-RA-A741 
"AMP PEAK  4(2Q32.3) WILD-TYPE" 
D4V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  4(2Q32.3) MUTATED                                             2
  AMP PEAK  4(2Q32.3) WILD-TYPE                                          19
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  4(2Q32.3) MUTATED                                        0
  AMP PEAK  4(2Q32.3) WILD-TYPE                                      8
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  4(2Q32.3) MUTATED                                                 1
  AMP PEAK  4(2Q32.3) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  4(2Q32.3) MUTATED                6                  14
  AMP PEAK  4(2Q32.3) WILD-TYPE             30                  69
D4V18, multiclass
                                                 clus
vv                                                AMP PEAK  4(2Q32.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                            6
  LIFELONG NON-SMOKER                                                      14
                                                 clus
vv                                                AMP PEAK  4(2Q32.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             30
  LIFELONG NON-SMOKER                                                        69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  4(2Q32.3) MUTATED             3        3             1        2
  AMP PEAK  4(2Q32.3) WILD-TYPE          14       34            10        3
D4V20, multiclass
               clus
vv              AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  COMBINATION                             3                            14
  EXTERNAL                                3                            34
  EXTERNAL BEAM                           1                            10
  INTERNAL                                2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V21, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q32.3) MUTATED    1  0
  AMP PEAK  4(2Q32.3) WILD-TYPE 10  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q32.3) MUTATED      1    0
  AMP PEAK  4(2Q32.3) WILD-TYPE   10    3
     clus
vv    AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  CGY                           1                            10
  GY                            0                             3
[1] 2 2
[1] FALSE
D4V22, continuous
D4V23, continuous
D4V24, continuous
D4V25, continuous
D4V26, continuous
D4V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  4(2Q32.3) MUTATED                                     0
  AMP PEAK  4(2Q32.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  4(2Q32.3) MUTATED                                     1
  AMP PEAK  4(2Q32.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  4(2Q32.3) MUTATED                         1                       0
  AMP PEAK  4(2Q32.3) WILD-TYPE                       8                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK  4(2Q32.3) MUTATED                         0
  AMP PEAK  4(2Q32.3) WILD-TYPE                       5
D4V28, multiclass
[1] "Remove cluster labels:"      "AMP PEAK  4(2Q32.3) MUTATED"
clus
  AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE 
                            2                            21 
                   TCGA-BI-A20A                    TCGA-C5-A1BE 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-C5-A1BM                    TCGA-C5-A2LX 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-DR-A0ZM                    TCGA-DS-A0VK 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-DS-A0VL                    TCGA-DS-A0VM 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-DS-A0VN                    TCGA-DS-A3LQ 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-EA-A50E                    TCGA-EK-A2RN 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-EX-A1H5 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-EX-A449                    TCGA-FU-A3EO 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-HM-A4S6                    TCGA-IR-A3LH 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-IR-A3LI                    TCGA-IR-A3LK 
"AMP PEAK  4(2Q32.3) WILD-TYPE" "AMP PEAK  4(2Q32.3) WILD-TYPE" 
                   TCGA-MU-A8JM 
"AMP PEAK  4(2Q32.3) WILD-TYPE" 
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  4(2Q32.3) MUTATED                                               0
  AMP PEAK  4(2Q32.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  4(2Q32.3) MUTATED                                                4
  AMP PEAK  4(2Q32.3) WILD-TYPE                                              6
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  4(2Q32.3) MUTATED                                                                                   6
  AMP PEAK  4(2Q32.3) WILD-TYPE                                                                                48
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  4(2Q32.3) MUTATED                                                                                             12
  AMP PEAK  4(2Q32.3) WILD-TYPE                                                                                           65
D4V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  4(2Q32.3) 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)                          12
                                                                                              clus
vv                                                                                             AMP PEAK  4(2Q32.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       48
  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"
D4V30, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q32.3) MUTATED    4 12
  AMP PEAK  4(2Q32.3) WILD-TYPE 50 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q32.3) MUTATED      4   12
  AMP PEAK  4(2Q32.3) WILD-TYPE   50   47
         clus
vv        AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  ABSENT                            4                            50
  PRESENT                          12                            47
[1] 2 2
[1] FALSE
D4V31, continuous
D4V32, continuous
D4V33, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q32.3) MUTATED    6  9
  AMP PEAK  4(2Q32.3) WILD-TYPE 29 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q32.3) MUTATED      6    9
  AMP PEAK  4(2Q32.3) WILD-TYPE   29   72
                                          clus
vv                                         AMP PEAK  4(2Q32.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           9
                                          clus
vv                                         AMP PEAK  4(2Q32.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            72
[1] 2 2
[1] FALSE
D4V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  4(2Q32.3) MUTATED       0                   15                   1
  AMP PEAK  4(2Q32.3) WILD-TYPE     3                   98                   4
D4V35, multiclass
                      clus
vv                     AMP PEAK  4(2Q32.3) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          15
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     AMP PEAK  4(2Q32.3) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            98
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK  4(2Q32.3) MUTATED              0           7          2
  AMP PEAK  4(2Q32.3) WILD-TYPE            8          33         38
D4V36, multiclass
              clus
vv             AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  CURRENT USER                           0                             8
  FORMER USER                            7                            33
  NEVER USED                             2                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V37, continuous
D4V38, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q32.3) MUTATED    8  2
  AMP PEAK  4(2Q32.3) WILD-TYPE 65 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q32.3) MUTATED      8    2
  AMP PEAK  4(2Q32.3) WILD-TYPE   65   12
         clus
vv        AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  ABSENT                            8                            65
  PRESENT                           2                            12
[1] 2 2
[1] FALSE
D4V39, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK  4(2Q32.3) MUTATED     0    0   2   10    1  0   1    2    1   0   0
  AMP PEAK  4(2Q32.3) WILD-TYPE   2    1  20   41   20  3   5    4    7  13   2
                               vv
clus                            T4 TX
  AMP PEAK  4(2Q32.3) MUTATED    0  0
  AMP PEAK  4(2Q32.3) WILD-TYPE  1  7
D4V40, multiclass
      clus
vv     AMP PEAK  4(2Q32.3) MUTATED AMP PEAK  4(2Q32.3) WILD-TYPE
  T1A                            0                             2
  T1A1                           0                             1
  T1B                            2                            20
  T1B1                          10                            41
  T1B2                           1                            20
  T2                             0                             3
  T2A                            1                             5
  T2A1                           2                             4
  T2A2                           1                             7
  T2B                            0                            13
  T3B                            0                             2
  T4                             0                             1
  TX                             0                             7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V41, continuous

Clustering(5) Variable = AMP PEAK  5(3Q26.31) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(3Q26.31) MUTATED   103  26
  AMP PEAK  5(3Q26.31) WILD-TYPE  34   6
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                           129                             40 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                            26                              6 
$`AMP PEAK  5(3Q26.31) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85         5.46        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-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
        0.82        18.02        17.85        20.42        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48         9.67        73.41        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VK 
       94.95         9.34        13.61         2.73        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH 
        2.66       117.99       118.65        22.98        16.83         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E 
        0.62        13.05         1.35        14.50        12.66         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       13.48        12.59         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        0.03        23.70         2.24         0.10         0.07         0.03 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI 
       20.35         6.94         4.47         6.12        23.84         1.45 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A2PA 
        1.48         0.82         3.52         1.35         1.97        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LC 
       21.67        20.78        14.93         4.11       137.16       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       78.71        81.96        36.36        19.33        20.48        15.58 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        5.13         0.10         0.89         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73R TCGA-R2-A69V 
        3.45         5.85         3.39         5.75         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

$`AMP PEAK  5(3Q26.31) WILD-TYPE`
TCGA-C5-A1BF TCGA-C5-A1BQ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7UC 
       18.74        19.86        38.43        52.01       182.93        17.19 
TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B 
       58.88        16.18         1.18        14.50         1.35         1.81 
TCGA-EA-A4BA TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RE TCGA-EK-A2RJ 
       12.82        13.58        45.96         6.64         0.36         1.18 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-FU-A23K TCGA-FU-A2QG 
        0.10         0.10         7.92        14.70         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-FU-A770 
        2.17         0.66         1.02         1.58         1.32         1.12 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI 
      147.39        66.81        96.95        26.56        14.43        16.64 
TCGA-JW-A69B TCGA-LP-A4AX TCGA-Q1-A6DV TCGA-Q1-A73P 
       10.06         0.07         3.72         4.80 

  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                        177.04                         182.93 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                         13.91                           8.99 
[1] "0.0 - 177.0 (13.9)" "0.1 - 182.9 (9.0)" 
[1] "hr=" "1"  
D5V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK  5(3Q26.31) MUTATED   69       30
  AMP PEAK  5(3Q26.31) WILD-TYPE 28        9
D5V3, multiclass
          clus
vv         AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  T1                                 69                             28
  T2+T3+T4                           30                              9
[1] 2 2
[1] FALSE
D5V4, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   59 34
  AMP PEAK  5(3Q26.31) WILD-TYPE 28  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     59   34
  AMP PEAK  5(3Q26.31) WILD-TYPE   28    6
   clus
vv  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  0                           59                             28
  1                           34                              6
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  5(3Q26.31) MUTATED   57  2 45
  AMP PEAK  5(3Q26.31) WILD-TYPE 15  1 20
D5V5, multiclass
    clus
vv   AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  M0                           57                             15
  M1                            2                              1
  MX                           45                             20
[1] 3 2
[1] 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
  AMP PEAK  5(3Q26.31) MUTATED               1                              116
  AMP PEAK  5(3Q26.31) WILD-TYPE             1                               28
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  5(3Q26.31) MUTATED                                               2
  AMP PEAK  5(3Q26.31) WILD-TYPE                                             2
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  5(3Q26.31) MUTATED                                    10
  AMP PEAK  5(3Q26.31) WILD-TYPE                                  10
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  5(3Q26.31) MUTATED                                           2
  AMP PEAK  5(3Q26.31) WILD-TYPE                                         0
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  5(3Q26.31) MUTATED                                              3
  AMP PEAK  5(3Q26.31) WILD-TYPE                                            1
D5V6, multiclass
                                               clus
vv                                              AMP PEAK  5(3Q26.31) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       116
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             3
                                               clus
vv                                              AMP PEAK  5(3Q26.31) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                          28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED    25 109
  AMP PEAK  5(3Q26.31) WILD-TYPE   2  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     25  109
  AMP PEAK  5(3Q26.31) WILD-TYPE    2   40
     clus
vv    AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  NO                            25                              2
  YES                          109                             40
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(3Q26.31) MUTATED                                  5    12
  AMP PEAK  5(3Q26.31) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(3Q26.31) MUTATED                          18
  AMP PEAK  5(3Q26.31) WILD-TYPE                         0
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  5(3Q26.31) MUTATED                                           0
  AMP PEAK  5(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK  5(3Q26.31) MUTATED      95
  AMP PEAK  5(3Q26.31) WILD-TYPE    35
D5V10, multiclass
                                           clus
vv                                          AMP PEAK  5(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               95
                                           clus
vv                                          AMP PEAK  5(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                  3
  BLACK OR AFRICAN AMERICAN                                              0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 35
[1] 5 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
  AMP PEAK  5(3Q26.31) MUTATED    7 99
  AMP PEAK  5(3Q26.31) WILD-TYPE  4 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED      7   99
  AMP PEAK  5(3Q26.31) WILD-TYPE    4   28
                        clus
vv                       AMP PEAK  5(3Q26.31) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       AMP PEAK  5(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             28
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   40 16
  AMP PEAK  5(3Q26.31) WILD-TYPE  8  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     40   16
  AMP PEAK  5(3Q26.31) WILD-TYPE    8    3
            clus
vv           AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  TUMOR FREE                           40                              8
  WITH TUMOR                           16                              3
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  5(3Q26.31) MUTATED         1      8       3           112      10
  AMP PEAK  5(3Q26.31) WILD-TYPE       0      2       3            35       2
D5V14, multiclass
               clus
vv              AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  NIGERIA                                  1                              0
  RUSSIA                                   8                              2
  UKRAINE                                  3                              3
  UNITED STATES                          112                             35
  VIETNAM                                 10                              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                             G1 G2 G3 G4 GX
  AMP PEAK  5(3Q26.31) MUTATED   10 65 53  1  4
  AMP PEAK  5(3Q26.31) WILD-TYPE  4 18 19  0  1
D5V15, multiclass
    clus
vv   AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  G1                           10                              4
  G2                           65                             18
  G3                           53                             19
  G4                            1                              0
  GX                            4                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V16, continuous
D5V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  5(3Q26.31) MUTATED                                            17
  AMP PEAK  5(3Q26.31) WILD-TYPE                                           4
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  5(3Q26.31) MUTATED                                        7
  AMP PEAK  5(3Q26.31) WILD-TYPE                                      1
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  5(3Q26.31) MUTATED                                                 1
  AMP PEAK  5(3Q26.31) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  5(3Q26.31) MUTATED               28                  64
  AMP PEAK  5(3Q26.31) WILD-TYPE              8                  19
D5V18, multiclass
                                                 clus
vv                                                AMP PEAK  5(3Q26.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            28
  LIFELONG NON-SMOKER                                                       64
                                                 clus
vv                                                AMP PEAK  5(3Q26.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                               8
  LIFELONG NON-SMOKER                                                         19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  5(3Q26.31) MUTATED            16       27            10        5
  AMP PEAK  5(3Q26.31) WILD-TYPE           1       10             1        0
D5V20, multiclass
               clus
vv              AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  COMBINATION                             16                              1
  EXTERNAL                                27                             10
  EXTERNAL BEAM                           10                              1
  INTERNAL                                 5                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V21, binary
                                cls
clus                             0 1
  AMP PEAK  5(3Q26.31) MUTATED   8 3
  AMP PEAK  5(3Q26.31) WILD-TYPE 3 0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED      8    3
  AMP PEAK  5(3Q26.31) WILD-TYPE    3    0
     clus
vv    AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  CGY                            8                              3
  GY                             3                              0
[1] 2 2
[1] FALSE
D5V22, continuous
D5V23, continuous
D5V24, continuous
D5V25, continuous
D5V26, continuous
D5V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  5(3Q26.31) MUTATED                                     1
  AMP PEAK  5(3Q26.31) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  5(3Q26.31) MUTATED                                     5
  AMP PEAK  5(3Q26.31) WILD-TYPE                                   1
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  5(3Q26.31) MUTATED                         8
  AMP PEAK  5(3Q26.31) WILD-TYPE                       1
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK  5(3Q26.31) MUTATED                         1
  AMP PEAK  5(3Q26.31) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK  5(3Q26.31) MUTATED                         4
  AMP PEAK  5(3Q26.31) WILD-TYPE                       1
D5V28, multiclass
                                     clus
vv                                    AMP PEAK  5(3Q26.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            5
  OTHER LOCATION, SPECIFY                                        8
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        4
                                     clus
vv                                    AMP PEAK  5(3Q26.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  OTHER LOCATION, SPECIFY                                          1
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  5(3Q26.31) MUTATED                                               2
  AMP PEAK  5(3Q26.31) WILD-TYPE                                             0
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  5(3Q26.31) MUTATED                                                7
  AMP PEAK  5(3Q26.31) WILD-TYPE                                              3
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  5(3Q26.31) MUTATED                                                                                  45
  AMP PEAK  5(3Q26.31) WILD-TYPE                                                                                 9
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  5(3Q26.31) MUTATED                                                                                             56
  AMP PEAK  5(3Q26.31) WILD-TYPE                                                                                           21
D5V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  5(3Q26.31) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           56
                                                                                              clus
vv                                                                                             AMP PEAK  5(3Q26.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V30, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   38 47
  AMP PEAK  5(3Q26.31) WILD-TYPE 16 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     38   47
  AMP PEAK  5(3Q26.31) WILD-TYPE   16   12
         clus
vv        AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  ABSENT                            38                             16
  PRESENT                           47                             12
[1] 2 2
[1] FALSE
D5V31, continuous
D5V32, continuous
D5V33, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   28 61
  AMP PEAK  5(3Q26.31) WILD-TYPE  7 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     28   61
  AMP PEAK  5(3Q26.31) WILD-TYPE    7   20
                                          clus
vv                                         AMP PEAK  5(3Q26.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           61
                                          clus
vv                                         AMP PEAK  5(3Q26.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             20
[1] 2 2
[1] FALSE
D5V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  5(3Q26.31) MUTATED       1                   85                   2
  AMP PEAK  5(3Q26.31) WILD-TYPE     2                   28                   3
D5V35, multiclass
                      clus
vv                     AMP PEAK  5(3Q26.31) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           85
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     AMP PEAK  5(3Q26.31) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             28
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  5(3Q26.31) MUTATED              5          29         29
  AMP PEAK  5(3Q26.31) WILD-TYPE            3          11         11
D5V36, multiclass
              clus
vv             AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  CURRENT USER                            5                              3
  FORMER USER                            29                             11
  NEVER USED                             29                             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"
D5V37, continuous
D5V38, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.31) MUTATED   53 11
  AMP PEAK  5(3Q26.31) WILD-TYPE 20  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     53   11
  AMP PEAK  5(3Q26.31) WILD-TYPE   20    3
         clus
vv        AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  ABSENT                            53                             20
  PRESENT                           11                              3
[1] 2 2
[1] FALSE
D5V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK  5(3Q26.31) MUTATED     2    1  17   35   14  3   5    6    4   9
  AMP PEAK  5(3Q26.31) WILD-TYPE   0    0   5   16    7  0   1    0    4   4
                                vv
clus                             T3B T4 TX
  AMP PEAK  5(3Q26.31) MUTATED     2  1  6
  AMP PEAK  5(3Q26.31) WILD-TYPE   0  0  1
D5V40, multiclass
      clus
vv     AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  T1A                             2                              0
  T1A1                            1                              0
  T1B                            17                              5
  T1B1                           35                             16
  T1B2                           14                              7
  T2                              3                              0
  T2A                             5                              1
  T2A1                            6                              0
  T2A2                            4                              4
  T2B                             9                              4
  T3B                             2                              0
  T4                              1                              0
  TX                              6                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V41, continuous

Clustering(6) Variable = AMP PEAK  6(3Q28) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  6(3Q28) MUTATED   103  25
  AMP PEAK  6(3Q28) WILD-TYPE  34   7
  AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE 
                        128                          41 
  AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE 
                         25                           7 
$`AMP PEAK  6(3Q28) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85         5.46        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-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
        0.82        18.02        17.85        20.42        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48         9.67        73.41        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VK 
       94.95         9.34        13.61         2.73        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH 
        2.66       117.99       118.65        22.98        16.83         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E 
        0.62        13.05         1.35        14.50        12.66         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       13.48        12.59         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN 
        0.03        23.70         2.24         0.10         0.07         0.03 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI 
       20.35         6.94         4.47         6.12        23.84         1.45 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A2PA 
        1.48         0.82         3.52         1.35         1.97        25.41 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
       20.78        14.93       137.16       117.40        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
       36.36        14.43        19.33        20.48        15.58         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.10         0.89         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        5.85         3.39         5.75         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

$`AMP PEAK  6(3Q28) WILD-TYPE`
TCGA-C5-A1BF TCGA-C5-A1BQ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7UC 
       18.74        19.86        38.43        52.01       182.93        17.19 
TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B 
       58.88        16.18         1.18        14.50         1.35         1.81 
TCGA-EA-A4BA TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RE TCGA-EK-A2RJ 
       12.82        13.58        45.96         6.64         0.36         1.18 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 TCGA-FU-A23K TCGA-FU-A2QG 
        0.10         0.10         7.92        14.70         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-FU-A770 
        2.17         0.66         1.02         1.58         1.32         1.12 
TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK 
       21.67         4.11       147.39        66.81        96.95        26.56 
TCGA-JW-A5VI TCGA-JW-A69B TCGA-LP-A4AX TCGA-Q1-A6DV TCGA-Q1-A73P 
       16.64        10.06         0.07         3.72         4.80 

  AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE 
                       0.03                        0.07 
  AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE 
                     177.04                      182.93 
  AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE 
                      14.17                        7.92 
[1] "0.0 - 177.0 (14.2)" "0.1 - 182.9 (7.9)" 
[1] "hr=" "1.2"
D6V2, continuous
                             vv
clus                          T1 T2+T3+T4
  AMP PEAK  6(3Q28) MUTATED   69       30
  AMP PEAK  6(3Q28) WILD-TYPE 28        9
D6V3, multiclass
          clus
vv         AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  T1                              69                          28
  T2+T3+T4                        30                           9
[1] 2 2
[1] FALSE
D6V4, binary
                             cls
clus                           0  1
  AMP PEAK  6(3Q28) MUTATED   59 33
  AMP PEAK  6(3Q28) WILD-TYPE 28  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(3Q28) MUTATED     59   33
  AMP PEAK  6(3Q28) WILD-TYPE   28    7
   clus
vv  AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  0                        59                          28
  1                        33                           7
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK  6(3Q28) MUTATED   57  1 46
  AMP PEAK  6(3Q28) WILD-TYPE 15  2 19
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  M0                        57                          15
  M1                         1                           2
  MX                        46                          19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(3Q28) MUTATED               0                              117
  AMP PEAK  6(3Q28) WILD-TYPE             2                               27
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  6(3Q28) MUTATED                                               2
  AMP PEAK  6(3Q28) WILD-TYPE                                             2
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  6(3Q28) MUTATED                                    10
  AMP PEAK  6(3Q28) WILD-TYPE                                  10
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  6(3Q28) MUTATED                                           2
  AMP PEAK  6(3Q28) WILD-TYPE                                         0
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  6(3Q28) MUTATED                                              3
  AMP PEAK  6(3Q28) WILD-TYPE                                            1
D6V6, multiclass
                                               clus
vv                                              AMP PEAK  6(3Q28) MUTATED
  ADENOSQUAMOUS                                                         0
  CERVICAL SQUAMOUS CELL CARCINOMA                                    117
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                  10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          3
                                               clus
vv                                              AMP PEAK  6(3Q28) WILD-TYPE
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                             cls
clus                            0   1
  AMP PEAK  6(3Q28) MUTATED    24 110
  AMP PEAK  6(3Q28) WILD-TYPE   3  39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(3Q28) MUTATED     24  110
  AMP PEAK  6(3Q28) WILD-TYPE    3   39
     clus
vv    AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  NO                         24                           3
  YES                       110                          39
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(3Q28) MUTATED                                  6    12
  AMP PEAK  6(3Q28) WILD-TYPE                                1     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(3Q28) MUTATED                          16
  AMP PEAK  6(3Q28) WILD-TYPE                         2
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(3Q28) MUTATED                                           0    96
  AMP PEAK  6(3Q28) WILD-TYPE                                         1    34
D6V10, multiclass
                                           clus
vv                                          AMP PEAK  6(3Q28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  6
  ASIAN                                                            12
  BLACK OR AFRICAN AMERICAN                                        16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            96
                                           clus
vv                                          AMP PEAK  6(3Q28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              34
[1] 5 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
  AMP PEAK  6(3Q28) MUTATED    8 98
  AMP PEAK  6(3Q28) WILD-TYPE  3 29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(3Q28) MUTATED      8   98
  AMP PEAK  6(3Q28) WILD-TYPE    3   29
                        clus
vv                       AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  HISPANIC OR LATINO                             8                           3
  NOT HISPANIC OR LATINO                        98                          29
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                             cls
clus                           0  1
  AMP PEAK  6(3Q28) MUTATED   40 15
  AMP PEAK  6(3Q28) WILD-TYPE  8  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(3Q28) MUTATED     40   15
  AMP PEAK  6(3Q28) WILD-TYPE    8    4
            clus
vv           AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  TUMOR FREE                        40                           8
  WITH TUMOR                        15                           4
[1] 2 2
[1] FALSE
                             vv
clus                          NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  6(3Q28) MUTATED         1      8       3           112      10
  AMP PEAK  6(3Q28) WILD-TYPE       0      2       3            35       2
D6V14, multiclass
               clus
vv              AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  NIGERIA                               1                           0
  RUSSIA                                8                           2
  UKRAINE                               3                           3
  UNITED STATES                       112                          35
  VIETNAM                              10                           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                          G1 G2 G3 G4 GX
  AMP PEAK  6(3Q28) MUTATED   10 65 53  1  4
  AMP PEAK  6(3Q28) WILD-TYPE  4 18 19  0  1
D6V15, multiclass
    clus
vv   AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  G1                        10                           4
  G2                        65                          18
  G3                        53                          19
  G4                         1                           0
  GX                         4                           1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V16, continuous
D6V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  6(3Q28) MUTATED                                            17
  AMP PEAK  6(3Q28) WILD-TYPE                                           4
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  6(3Q28) MUTATED                                        7
  AMP PEAK  6(3Q28) WILD-TYPE                                      1
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  6(3Q28) MUTATED                                                 1
  AMP PEAK  6(3Q28) WILD-TYPE                                               0
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  6(3Q28) MUTATED               27                  65
  AMP PEAK  6(3Q28) WILD-TYPE              9                  18
D6V18, multiclass
                                                 clus
vv                                                AMP PEAK  6(3Q28) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                            17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         1
  CURRENT SMOKER                                                         27
  LIFELONG NON-SMOKER                                                    65
                                                 clus
vv                                                AMP PEAK  6(3Q28) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                            9
  LIFELONG NON-SMOKER                                                      18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V19, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  6(3Q28) MUTATED            16       27             9        5
  AMP PEAK  6(3Q28) WILD-TYPE           1       10             2        0
D6V20, multiclass
               clus
vv              AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  COMBINATION                          16                           1
  EXTERNAL                             27                          10
  EXTERNAL BEAM                         9                           2
  INTERNAL                              5                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V21, binary
                             cls
clus                          0 1
  AMP PEAK  6(3Q28) MUTATED   8 3
  AMP PEAK  6(3Q28) WILD-TYPE 3 0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(3Q28) MUTATED      8    3
  AMP PEAK  6(3Q28) WILD-TYPE    3    0
     clus
vv    AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  CGY                         8                           3
  GY                          3                           0
[1] 2 2
[1] FALSE
D6V22, continuous
D6V23, continuous
D6V24, continuous
D6V25, continuous
D6V26, continuous
D6V27, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  6(3Q28) MUTATED                                     1
  AMP PEAK  6(3Q28) WILD-TYPE                                   1
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  6(3Q28) MUTATED                                     5
  AMP PEAK  6(3Q28) WILD-TYPE                                   1
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  6(3Q28) MUTATED                         8                       1
  AMP PEAK  6(3Q28) WILD-TYPE                       1                       0
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  6(3Q28) MUTATED                         4
  AMP PEAK  6(3Q28) WILD-TYPE                       1
D6V28, multiclass
                                     clus
vv                                    AMP PEAK  6(3Q28) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         5
  OTHER LOCATION, SPECIFY                                     8
  POSITIVE BLADDER MARGIN                                     1
  POSITIVE VAGINAL MARGIN                                     4
                                     clus
vv                                    AMP PEAK  6(3Q28) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                       1
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  6(3Q28) MUTATED                                               2
  AMP PEAK  6(3Q28) WILD-TYPE                                             0
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  6(3Q28) MUTATED                                                7
  AMP PEAK  6(3Q28) WILD-TYPE                                              3
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  6(3Q28) MUTATED                                                                                  46
  AMP PEAK  6(3Q28) WILD-TYPE                                                                                 8
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  6(3Q28) MUTATED                                                                                             55
  AMP PEAK  6(3Q28) WILD-TYPE                                                                                           22
D6V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  6(3Q28) MUTATED
  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)                                   46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        55
                                                                                              clus
vv                                                                                             AMP PEAK  6(3Q28) WILD-TYPE
  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)                          22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V30, binary
                             cls
clus                           0  1
  AMP PEAK  6(3Q28) MUTATED   39 45
  AMP PEAK  6(3Q28) WILD-TYPE 15 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(3Q28) MUTATED     39   45
  AMP PEAK  6(3Q28) WILD-TYPE   15   14
         clus
vv        AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  ABSENT                         39                          15
  PRESENT                        45                          14
[1] 2 2
[1] FALSE
D6V31, continuous
D6V32, continuous
D6V33, binary
                             cls
clus                           0  1
  AMP PEAK  6(3Q28) MUTATED   28 62
  AMP PEAK  6(3Q28) WILD-TYPE  7 19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(3Q28) MUTATED     28   62
  AMP PEAK  6(3Q28) WILD-TYPE    7   19
                                          clus
vv                                         AMP PEAK  6(3Q28) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        62
                                          clus
vv                                         AMP PEAK  6(3Q28) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          19
[1] 2 2
[1] FALSE
D6V34, continuous
                             vv
clus                          OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  6(3Q28) MUTATED       1                   84                   2
  AMP PEAK  6(3Q28) WILD-TYPE     2                   29                   3
D6V35, multiclass
                      clus
vv                     AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  OTHER                                        1                           2
  RADICAL HYSTERECTOMY                        84                          29
  SIMPLE HYSTERECTOMY                          2                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  6(3Q28) MUTATED              5          27         30
  AMP PEAK  6(3Q28) WILD-TYPE            3          13         10
D6V36, multiclass
              clus
vv             AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  CURRENT USER                         5                           3
  FORMER USER                         27                          13
  NEVER USED                          30                          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"
D6V37, continuous
D6V38, binary
                             cls
clus                           0  1
  AMP PEAK  6(3Q28) MUTATED   53 11
  AMP PEAK  6(3Q28) WILD-TYPE 20  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(3Q28) MUTATED     53   11
  AMP PEAK  6(3Q28) WILD-TYPE   20    3
         clus
vv        AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  ABSENT                         53                          20
  PRESENT                        11                           3
[1] 2 2
[1] FALSE
D6V39, continuous
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK  6(3Q28) MUTATED     2    1  17   35   14  3   5    6    4   9   2
  AMP PEAK  6(3Q28) WILD-TYPE   0    0   5   16    7  0   1    0    4   4   0
                             vv
clus                          T4 TX
  AMP PEAK  6(3Q28) MUTATED    1  6
  AMP PEAK  6(3Q28) WILD-TYPE  0  1
D6V40, multiclass
      clus
vv     AMP PEAK  6(3Q28) MUTATED AMP PEAK  6(3Q28) WILD-TYPE
  T1A                          2                           0
  T1A1                         1                           0
  T1B                         17                           5
  T1B1                        35                          16
  T1B2                        14                           7
  T2                           3                           0
  T2A                          5                           1
  T2A1                         6                           0
  T2A2                         4                           4
  T2B                          9                           4
  T3B                          2                           0
  T4                           1                           0
  TX                           6                           1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V41, continuous

Clustering(7) Variable = AMP PEAK  7(4Q12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(4Q12) MUTATED     9   2
  AMP PEAK  7(4Q12) WILD-TYPE 128  30
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                         11                         158 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                          2                          30 
$`AMP PEAK  7(4Q12) MUTATED`
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MN TCGA-C5-A1MP TCGA-DS-A3LQ TCGA-EK-A2GZ 
       35.01        53.16        40.93         3.58        22.98        12.59 
TCGA-EK-A3GK TCGA-FU-A23K TCGA-IR-A3LF TCGA-IR-A3LH TCGA-MY-A5BF 
        0.10         1.22        96.95        78.71         4.34 

$`AMP PEAK  7(4Q12) 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-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LS TCGA-C5-A2LT 
       38.99        35.61         0.46         2.43        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       182.93        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       85.55        60.69        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         0.26        14.89         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.99        14.96        13.58        13.48        45.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.53         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-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-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.12        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.07         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                       0.10                        0.03 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                      96.95                      182.93 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                      22.98                       13.53 
[1] "0.1 - 97.0 (23.0)"  "0.0 - 182.9 (13.5)"
[1] "hr=" "1.2"
D7V2, continuous
                             vv
clus                          T1 T2+T3+T4
  AMP PEAK  7(4Q12) MUTATED    5        4
  AMP PEAK  7(4Q12) WILD-TYPE 92       35
D7V3, multiclass
          clus
vv         AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  T1                               5                          92
  T2+T3+T4                         4                          35
[1] 2 2
[1] FALSE
D7V4, binary
                             cls
clus                           0  1
  AMP PEAK  7(4Q12) MUTATED    5  4
  AMP PEAK  7(4Q12) WILD-TYPE 82 36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      5    4
  AMP PEAK  7(4Q12) WILD-TYPE   82   36
   clus
vv  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  0                         5                          82
  1                         4                          36
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK  7(4Q12) MUTATED    4  0  5
  AMP PEAK  7(4Q12) WILD-TYPE 68  3 60
D7V5, multiclass
    clus
vv   AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  M0                         4                          68
  M1                         0                           3
  MX                         5                          60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(4Q12) MUTATED               0                                9
  AMP PEAK  7(4Q12) WILD-TYPE             2                              135
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  7(4Q12) MUTATED                                               1
  AMP PEAK  7(4Q12) WILD-TYPE                                             3
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  7(4Q12) MUTATED                                     2
  AMP PEAK  7(4Q12) WILD-TYPE                                  18
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  7(4Q12) MUTATED                                           0
  AMP PEAK  7(4Q12) WILD-TYPE                                         2
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  7(4Q12) MUTATED                                              0
  AMP PEAK  7(4Q12) WILD-TYPE                                            4
D7V6, multiclass
                                               clus
vv                                              AMP PEAK  7(4Q12) 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                                              AMP PEAK  7(4Q12) WILD-TYPE
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      135
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED     4   8
  AMP PEAK  7(4Q12) WILD-TYPE  23 141
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      4    8
  AMP PEAK  7(4Q12) WILD-TYPE   23  141
     clus
vv    AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  NO                          4                          23
  YES                         8                         141
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(4Q12) MUTATED                                  0     0
  AMP PEAK  7(4Q12) WILD-TYPE                                7    15
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(4Q12) MUTATED                           3
  AMP PEAK  7(4Q12) WILD-TYPE                        15
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(4Q12) MUTATED                                           0     8
  AMP PEAK  7(4Q12) WILD-TYPE                                         1   122
D7V10, multiclass
                                           clus
vv                                          AMP PEAK  7(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  0
  ASIAN                                                             0
  BLACK OR AFRICAN AMERICAN                                         3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                             8
                                           clus
vv                                          AMP PEAK  7(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    7
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED     0   7
  AMP PEAK  7(4Q12) WILD-TYPE  11 120
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      0    7
  AMP PEAK  7(4Q12) WILD-TYPE   11  120
                        clus
vv                       AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                          11
  NOT HISPANIC OR LATINO                         7                         120
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                             cls
clus                           0  1
  AMP PEAK  7(4Q12) MUTATED    4  1
  AMP PEAK  7(4Q12) WILD-TYPE 44 18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      4    1
  AMP PEAK  7(4Q12) WILD-TYPE   44   18
            clus
vv           AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  TUMOR FREE                         4                          44
  WITH TUMOR                         1                          18
[1] 2 2
[1] FALSE
                             vv
clus                          NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  7(4Q12) MUTATED         0      0       0            12       0
  AMP PEAK  7(4Q12) WILD-TYPE       1     10       6           135      12
D7V14, multiclass
               clus
vv              AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  NIGERIA                               0                           1
  RUSSIA                                0                          10
  UKRAINE                               0                           6
  UNITED STATES                        12                         135
  VIETNAM                               0                          12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  AMP PEAK  7(4Q12) MUTATED    1  5  5  1  0
  AMP PEAK  7(4Q12) WILD-TYPE 13 78 67  0  5
D7V15, multiclass
    clus
vv   AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  G1                         1                          13
  G2                         5                          78
  G3                         5                          67
  G4                         1                           0
  GX                         0                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V16, continuous
D7V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  7(4Q12) MUTATED                                             2
  AMP PEAK  7(4Q12) WILD-TYPE                                          19
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  7(4Q12) MUTATED                                        1
  AMP PEAK  7(4Q12) WILD-TYPE                                      7
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  7(4Q12) MUTATED                                                 0
  AMP PEAK  7(4Q12) WILD-TYPE                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  7(4Q12) MUTATED                1                   5
  AMP PEAK  7(4Q12) WILD-TYPE             35                  78
D7V18, multiclass
                                                 clus
vv                                                AMP PEAK  7(4Q12) 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                                                          1
  LIFELONG NON-SMOKER                                                     5
                                                 clus
vv                                                AMP PEAK  7(4Q12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           35
  LIFELONG NON-SMOKER                                                      78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V19, continuous
[1] "Remove cluster labels:"    "AMP PEAK  7(4Q12) MUTATED"
clus
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                          2                          46 
                 TCGA-BI-A0VR                  TCGA-C5-A1BI 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A1BJ                  TCGA-C5-A1BL 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A1BN                  TCGA-C5-A1BQ 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A1M7                  TCGA-C5-A1ME 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A1MI                  TCGA-C5-A2LS 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A2LT                  TCGA-C5-A2LV 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A2LX                  TCGA-C5-A2LZ 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A2M2                  TCGA-C5-A3HD 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A3HF                  TCGA-C5-A7CJ 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A7CL                  TCGA-C5-A7CO 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A7UE                  TCGA-C5-A7X8 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-DR-A0ZM                  TCGA-DS-A5RQ 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-EA-A556                  TCGA-EX-A1H5 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-FU-A2QG                  TCGA-FU-A3EO 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-FU-A3HY                  TCGA-FU-A3TQ 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-FU-A3TX                  TCGA-FU-A3WB 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-FU-A3YQ                  TCGA-FU-A5XV 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-FU-A770                  TCGA-HM-A4S6 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-HM-A6W2                  TCGA-IR-A3L7 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-IR-A3LB                  TCGA-JW-A5VI 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-JW-A5VK                  TCGA-MU-A5YI 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-MU-A8JM                  TCGA-Q1-A6DW 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-RA-A741                  TCGA-UC-A7PD 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  7(4Q12) MUTATED             2        2             2        0
  AMP PEAK  7(4Q12) WILD-TYPE          15       35             9        5
D7V20, multiclass
               clus
vv              AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  COMBINATION                           2                          15
  EXTERNAL                              2                          35
  EXTERNAL BEAM                         2                           9
  INTERNAL                              0                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V21, binary
                             cls
clus                          0 1
  AMP PEAK  7(4Q12) MUTATED   2 0
  AMP PEAK  7(4Q12) WILD-TYPE 9 3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      2    0
  AMP PEAK  7(4Q12) WILD-TYPE    9    3
     clus
vv    AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  CGY                         2                           9
  GY                          0                           3
[1] 2 2
[1] FALSE
D7V22, continuous
D7V23, continuous
D7V24, continuous
D7V25, continuous
D7V26, continuous
D7V27, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  7(4Q12) MUTATED                                     0
  AMP PEAK  7(4Q12) WILD-TYPE                                   2
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  7(4Q12) MUTATED                                     0
  AMP PEAK  7(4Q12) WILD-TYPE                                   6
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK  7(4Q12) MUTATED                         1                       0
  AMP PEAK  7(4Q12) WILD-TYPE                       8                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK  7(4Q12) MUTATED                         1
  AMP PEAK  7(4Q12) WILD-TYPE                       4
D7V28, multiclass
[1] "Remove cluster labels:"    "AMP PEAK  7(4Q12) MUTATED"
clus
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                          2                          21 
                 TCGA-BI-A20A                  TCGA-C5-A0TN 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A1BE                  TCGA-C5-A1BM 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-C5-A2LX                  TCGA-DR-A0ZM 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-DS-A0VK                  TCGA-DS-A0VL 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-DS-A0VM                  TCGA-DS-A0VN 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-EA-A50E                  TCGA-EK-A2RN 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-EK-A2RO                  TCGA-EX-A1H5 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-EX-A449                  TCGA-FU-A3EO 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-HM-A4S6                  TCGA-IR-A3LI 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-IR-A3LK                  TCGA-MU-A8JM 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-UC-A7PD 
"AMP PEAK  7(4Q12) WILD-TYPE" 
                             vv
clus                          INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK  7(4Q12) MUTATED                                               0
  AMP PEAK  7(4Q12) WILD-TYPE                                             2
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  7(4Q12) MUTATED                                                0
  AMP PEAK  7(4Q12) WILD-TYPE                                             10
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  7(4Q12) MUTATED                                                                                   3
  AMP PEAK  7(4Q12) WILD-TYPE                                                                                51
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  7(4Q12) MUTATED                                                                                              7
  AMP PEAK  7(4Q12) WILD-TYPE                                                                                           70
D7V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  7(4Q12) 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)                         7
                                                                                              clus
vv                                                                                             AMP PEAK  7(4Q12) 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)                          70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V30, binary
                             cls
clus                           0  1
  AMP PEAK  7(4Q12) MUTATED    3  6
  AMP PEAK  7(4Q12) WILD-TYPE 51 53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      3    6
  AMP PEAK  7(4Q12) WILD-TYPE   51   53
         clus
vv        AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  ABSENT                          3                          51
  PRESENT                         6                          53
[1] 2 2
[1] FALSE
D7V31, continuous
D7V32, continuous
D7V33, binary
                             cls
clus                           0  1
  AMP PEAK  7(4Q12) MUTATED    2  3
  AMP PEAK  7(4Q12) WILD-TYPE 33 78
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      2    3
  AMP PEAK  7(4Q12) WILD-TYPE   33   78
                                          clus
vv                                         AMP PEAK  7(4Q12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         3
                                          clus
vv                                         AMP PEAK  7(4Q12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          78
[1] 2 2
[1] FALSE
D7V34, continuous
                             vv
clus                          OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  7(4Q12) MUTATED       1                    7                   1
  AMP PEAK  7(4Q12) WILD-TYPE     2                  106                   4
D7V35, multiclass
                      clus
vv                     AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  OTHER                                        1                           2
  RADICAL HYSTERECTOMY                         7                         106
  SIMPLE HYSTERECTOMY                          1                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK  7(4Q12) MUTATED              1           5          1
  AMP PEAK  7(4Q12) WILD-TYPE            7          35         39
D7V36, multiclass
              clus
vv             AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  CURRENT USER                         1                           7
  FORMER USER                          5                          35
  NEVER USED                           1                          39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V37, continuous
D7V38, binary
                             cls
clus                           0  1
  AMP PEAK  7(4Q12) MUTATED    5  0
  AMP PEAK  7(4Q12) WILD-TYPE 68 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      5    0
  AMP PEAK  7(4Q12) WILD-TYPE   68   14
         clus
vv        AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  ABSENT                          5                          68
  PRESENT                         0                          14
[1] 2 2
[1] FALSE
D7V39, continuous
[1] "Remove cluster labels:"    "AMP PEAK  7(4Q12) MUTATED"
clus
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                          2                           7 
                 TCGA-C5-A1BN                  TCGA-C5-A1MH 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-EK-A2RO                  TCGA-HM-A3JK 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-JW-A852                  TCGA-MU-A51Y 
"AMP PEAK  7(4Q12) WILD-TYPE" "AMP PEAK  7(4Q12) WILD-TYPE" 
                 TCGA-MU-A8JM 
"AMP PEAK  7(4Q12) WILD-TYPE" 
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK  7(4Q12) MUTATED     0    0   0    3    2  0   0    1    1   0   2
  AMP PEAK  7(4Q12) WILD-TYPE   2    1  22   48   19  3   6    5    7  13   0
                             vv
clus                          T4 TX
  AMP PEAK  7(4Q12) MUTATED    0  0
  AMP PEAK  7(4Q12) WILD-TYPE  1  7
D7V40, multiclass
      clus
vv     AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  T1A                          0                           2
  T1A1                         0                           1
  T1B                          0                          22
  T1B1                         3                          48
  T1B2                         2                          19
  T2                           0                           3
  T2A                          0                           6
  T2A1                         1                           5
  T2A2                         1                           7
  T2B                          0                          13
  T3B                          2                           0
  T4                           0                           1
  TX                           0                           7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V41, continuous

Clustering(8) Variable = AMP PEAK  8(5P15.33) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(5P15.33) MUTATED   57 11
  AMP PEAK  8(5P15.33) WILD-TYPE 80 21
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            68                            101 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            11                             21 
$`AMP PEAK  8(5P15.33) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BQ 
       49.48        57.04        11.44       144.16       173.29        19.86 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT 
       31.40        46.32        57.73        40.93         3.58        73.18 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CM 
      100.14        38.43        52.01        18.02        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X8 
       73.41        17.19        85.55        60.69         9.34         2.73 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3Y4 
        2.66       117.99        22.98         0.76         1.32        14.50 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A78R 
       14.50         1.81        14.89        13.91        14.96        13.48 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN 
       45.96         0.53         0.59         1.18         2.24         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L 
        0.10         0.03        20.35         6.94         4.47        23.84 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3LH 
        0.66         1.45         1.97        25.41        21.67        78.71 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A852 TCGA-LP-A4AW 
       26.56        36.36        14.43        16.64         5.13         0.89 
TCGA-LP-A5U3 TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.82         0.07         2.96         3.45         5.85         3.39 
TCGA-Q1-A6DW TCGA-UC-A7PD 
        5.75        11.67 

$`AMP PEAK  8(5P15.33) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM 
       23.67        68.84        18.74        36.56       177.04        82.85 
TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH 
        5.46        67.46        30.21        35.01        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       35.61         0.46         2.43        44.22        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       78.35         0.82        17.85        20.42       182.93        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM 
      101.82       134.33        94.95        13.61        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       36.76       118.65        16.83        16.18         7.33         8.28 
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-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35         1.35        12.66        12.82         0.26         1.48 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2RB 
        0.69        14.99        13.58        12.59         6.64         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ 
        4.04         0.03         0.36        23.70         0.07         0.10 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92        14.70         6.12         1.22         0.92         2.17 
TCGA-FU-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-A770 TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.32         1.12        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VJ 
      137.16        66.81       117.40        96.95        81.96        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MU-A51Y 
       20.48        15.58        10.06         0.10         0.07        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A6DV 
        0.03         5.42        29.72         4.34         3.72         3.72 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        93.99 

  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                        173.29                         182.93 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                        14.465                         12.820 
[1] "0.0 - 173.3 (14.5)" "0.0 - 182.9 (12.8)"
[1] "hr=" "1.2"
D8V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK  8(5P15.33) MUTATED   36       14
  AMP PEAK  8(5P15.33) WILD-TYPE 61       25
D8V3, multiclass
          clus
vv         AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T1                                 36                             61
  T2+T3+T4                           14                             25
[1] 2 2
[1] FALSE
D8V4, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   31 15
  AMP PEAK  8(5P15.33) WILD-TYPE 56 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     31   15
  AMP PEAK  8(5P15.33) WILD-TYPE   56   25
   clus
vv  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  0                           31                             56
  1                           15                             25
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  8(5P15.33) MUTATED   32  0 22
  AMP PEAK  8(5P15.33) WILD-TYPE 40  3 43
D8V5, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  M0                           32                             40
  M1                            0                              3
  MX                           22                             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"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(5P15.33) MUTATED               0                               68
  AMP PEAK  8(5P15.33) WILD-TYPE             2                               76
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  8(5P15.33) MUTATED                                               1
  AMP PEAK  8(5P15.33) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  8(5P15.33) MUTATED                                     4
  AMP PEAK  8(5P15.33) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  8(5P15.33) MUTATED                                           1
  AMP PEAK  8(5P15.33) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  8(5P15.33) MUTATED                                              1
  AMP PEAK  8(5P15.33) WILD-TYPE                                            3
D8V6, multiclass
                                               clus
vv                                              AMP PEAK  8(5P15.33) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        68
  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                                              AMP PEAK  8(5P15.33) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          76
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED    9 66
  AMP PEAK  8(5P15.33) WILD-TYPE 18 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      9   66
  AMP PEAK  8(5P15.33) WILD-TYPE   18   83
     clus
vv    AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  NO                             9                             18
  YES                           66                             83
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(5P15.33) MUTATED                                  3     7
  AMP PEAK  8(5P15.33) WILD-TYPE                                4     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(5P15.33) MUTATED                           8
  AMP PEAK  8(5P15.33) WILD-TYPE                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  8(5P15.33) MUTATED                                           0
  AMP PEAK  8(5P15.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK  8(5P15.33) MUTATED      56
  AMP PEAK  8(5P15.33) WILD-TYPE    74
D8V10, multiclass
                                           clus
vv                                          AMP PEAK  8(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               56
                                           clus
vv                                          AMP PEAK  8(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                  8
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 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"
D8V11, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED    5 52
  AMP PEAK  8(5P15.33) WILD-TYPE  6 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      5   52
  AMP PEAK  8(5P15.33) WILD-TYPE    6   75
                        clus
vv                       AMP PEAK  8(5P15.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       AMP PEAK  8(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             75
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   21  6
  AMP PEAK  8(5P15.33) WILD-TYPE 27 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     21    6
  AMP PEAK  8(5P15.33) WILD-TYPE   27   13
            clus
vv           AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  TUMOR FREE                           21                             27
  WITH TUMOR                            6                             13
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  8(5P15.33) MUTATED         1      3       3            62       6
  AMP PEAK  8(5P15.33) WILD-TYPE       0      7       3            85       6
D8V14, multiclass
               clus
vv              AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  NIGERIA                                  1                              0
  RUSSIA                                   3                              7
  UKRAINE                                  3                              3
  UNITED STATES                           62                             85
  VIETNAM                                  6                              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                             G1 G2 G3 G4 GX
  AMP PEAK  8(5P15.33) MUTATED    2 32 37  1  2
  AMP PEAK  8(5P15.33) WILD-TYPE 12 51 35  0  3
D8V15, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  G1                            2                             12
  G2                           32                             51
  G3                           37                             35
  G4                            1                              0
  GX                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V16, continuous
D8V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  8(5P15.33) MUTATED                                             9
  AMP PEAK  8(5P15.33) WILD-TYPE                                          12
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  8(5P15.33) MUTATED                                        2
  AMP PEAK  8(5P15.33) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  8(5P15.33) MUTATED                                                 0
  AMP PEAK  8(5P15.33) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  8(5P15.33) MUTATED               16                  32
  AMP PEAK  8(5P15.33) WILD-TYPE             20                  51
D8V18, multiclass
                                                 clus
vv                                                AMP PEAK  8(5P15.33) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            16
  LIFELONG NON-SMOKER                                                       32
                                                 clus
vv                                                AMP PEAK  8(5P15.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              20
  LIFELONG NON-SMOKER                                                         51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  8(5P15.33) MUTATED             4       19             4        4
  AMP PEAK  8(5P15.33) WILD-TYPE          13       18             7        1
D8V20, multiclass
               clus
vv              AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  COMBINATION                              4                             13
  EXTERNAL                                19                             18
  EXTERNAL BEAM                            4                              7
  INTERNAL                                 4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V21, binary
                                cls
clus                             0 1
  AMP PEAK  8(5P15.33) MUTATED   8 1
  AMP PEAK  8(5P15.33) WILD-TYPE 3 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      8    1
  AMP PEAK  8(5P15.33) WILD-TYPE    3    2
     clus
vv    AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  CGY                            8                              3
  GY                             1                              2
[1] 2 2
[1] FALSE
D8V22, continuous
D8V23, continuous
D8V24, continuous
D8V25, continuous
D8V26, continuous
D8V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  8(5P15.33) MUTATED                                     0
  AMP PEAK  8(5P15.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  8(5P15.33) MUTATED                                     3
  AMP PEAK  8(5P15.33) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  8(5P15.33) MUTATED                         5
  AMP PEAK  8(5P15.33) WILD-TYPE                       4
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK  8(5P15.33) MUTATED                         0
  AMP PEAK  8(5P15.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK  8(5P15.33) MUTATED                         1
  AMP PEAK  8(5P15.33) WILD-TYPE                       4
D8V28, multiclass
                                     clus
vv                                    AMP PEAK  8(5P15.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                        5
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK  8(5P15.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              3
  OTHER LOCATION, SPECIFY                                          4
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  AMP PEAK  8(5P15.33) MUTATED                                               0
  AMP PEAK  8(5P15.33) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  8(5P15.33) MUTATED                                                3
  AMP PEAK  8(5P15.33) WILD-TYPE                                              7
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  8(5P15.33) MUTATED                                                                                  21
  AMP PEAK  8(5P15.33) WILD-TYPE                                                                                33
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  8(5P15.33) MUTATED                                                                                             34
  AMP PEAK  8(5P15.33) WILD-TYPE                                                                                           43
D8V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  8(5P15.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           34
                                                                                              clus
vv                                                                                             AMP PEAK  8(5P15.33) 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)                                        33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V30, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   19 23
  AMP PEAK  8(5P15.33) WILD-TYPE 35 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     19   23
  AMP PEAK  8(5P15.33) WILD-TYPE   35   36
         clus
vv        AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  ABSENT                            19                             35
  PRESENT                           23                             36
[1] 2 2
[1] FALSE
D8V31, continuous
D8V32, continuous
D8V33, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   12 39
  AMP PEAK  8(5P15.33) WILD-TYPE 23 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     12   39
  AMP PEAK  8(5P15.33) WILD-TYPE   23   42
                                          clus
vv                                         AMP PEAK  8(5P15.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           39
                                          clus
vv                                         AMP PEAK  8(5P15.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             42
[1] 2 2
[1] FALSE
D8V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  8(5P15.33) MUTATED       0                   43                   1
  AMP PEAK  8(5P15.33) WILD-TYPE     3                   70                   4
D8V35, multiclass
                      clus
vv                     AMP PEAK  8(5P15.33) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           43
  SIMPLE HYSTERECTOMY                             1
                      clus
vv                     AMP PEAK  8(5P15.33) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             70
  SIMPLE HYSTERECTOMY                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  8(5P15.33) MUTATED              4          17         14
  AMP PEAK  8(5P15.33) WILD-TYPE            4          23         26
D8V36, multiclass
              clus
vv             AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  CURRENT USER                            4                              4
  FORMER USER                            17                             23
  NEVER USED                             14                             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V37, continuous
D8V38, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   25  4
  AMP PEAK  8(5P15.33) WILD-TYPE 48 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     25    4
  AMP PEAK  8(5P15.33) WILD-TYPE   48   10
         clus
vv        AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  ABSENT                            25                             48
  PRESENT                            4                             10
[1] 2 2
[1] FALSE
D8V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK  8(5P15.33) MUTATED     2    0   8   18    8  0   3    4    0   6
  AMP PEAK  8(5P15.33) WILD-TYPE   0    1  14   33   13  3   3    2    8   7
                                vv
clus                             T3B T4 TX
  AMP PEAK  8(5P15.33) MUTATED     1  0  5
  AMP PEAK  8(5P15.33) WILD-TYPE   1  1  2
D8V40, multiclass
      clus
vv     AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T1A                             2                              0
  T1A1                            0                              1
  T1B                             8                             14
  T1B1                           18                             33
  T1B2                            8                             13
  T2                              0                              3
  T2A                             3                              3
  T2A1                            4                              2
  T2A2                            0                              8
  T2B                             6                              7
  T3B                             1                              1
  T4                              0                              1
  TX                              5                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V41, continuous

Clustering(9) Variable = AMP PEAK  9(6P21.33) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(6P21.33) MUTATED    34  11
  AMP PEAK  9(6P21.33) WILD-TYPE 103  21
  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE 
                            45                            124 
  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE 
                            11                             21 
$`AMP PEAK  9(6P21.33) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        57.04        11.44         5.46        31.40        46.32 
TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A3HE 
       35.01        38.99        35.61        78.35        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 
       17.85        25.35        85.55        60.69        94.95         2.73 
TCGA-DS-A0VM TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A43B 
      117.99         7.33         8.28         0.76        14.50         1.81 
TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GJ 
       14.89        13.91        14.96         1.18         2.24         0.10 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A57G TCGA-HG-A2PA TCGA-IR-A3LF 
        6.12         1.22        23.84         1.32        25.41        96.95 
TCGA-IR-A3LH TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MU-A5YI TCGA-MY-A5BD TCGA-PN-A8MA 
       78.71         0.10         0.07         0.03        29.72         2.96 
TCGA-Q1-A5R2 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.45        11.67        93.99 

$`AMP PEAK  9(6P21.33) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       23.67        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1ME 
      173.29        82.85        19.86        67.46        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       53.16         0.46         2.43        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.18        73.45        83.05       100.14        38.43         0.82 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       73.41        17.19         9.34        13.61        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       118.65        22.98        16.83        16.18 
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-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        0.26         1.48         0.69        14.99        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       12.59        45.96         6.64         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        4.04         0.03         0.36        23.70         0.10         0.07 
TCGA-EK-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-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        4.47         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-A5XV 
        1.58         1.48         0.82         3.52         1.35         1.97 
TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.12        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      137.16        66.81       117.40        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BE 
        5.13         0.89         0.82        13.87         5.42         0.07 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         3.72         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        4.80         6.25        19.59         3.88 

  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE 
                        117.99                         182.93 
  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE 
                         14.96                          12.74 
[1] "0.0 - 118.0 (15.0)" "0.0 - 182.9 (12.7)"
[1] "hr=" "1.4"
D9V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK  9(6P21.33) MUTATED   25       10
  AMP PEAK  9(6P21.33) WILD-TYPE 72       29
D9V3, multiclass
          clus
vv         AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  T1                                 25                             72
  T2+T3+T4                           10                             29
[1] 2 2
[1] FALSE
D9V4, binary
                                cls
clus                              0  1
  AMP PEAK  9(6P21.33) MUTATED   23 10
  AMP PEAK  9(6P21.33) WILD-TYPE 64 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(6P21.33) MUTATED     23   10
  AMP PEAK  9(6P21.33) WILD-TYPE   64   30
   clus
vv  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  0                           23                             64
  1                           10                             30
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  9(6P21.33) MUTATED   24  0 11
  AMP PEAK  9(6P21.33) WILD-TYPE 48  3 54
D9V5, multiclass
    clus
vv   AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  M0                           24                             48
  M1                            0                              3
  MX                           11                             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(6P21.33) MUTATED               0                               41
  AMP PEAK  9(6P21.33) WILD-TYPE             2                              103
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK  9(6P21.33) MUTATED                                               1
  AMP PEAK  9(6P21.33) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK  9(6P21.33) MUTATED                                     3
  AMP PEAK  9(6P21.33) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK  9(6P21.33) MUTATED                                           1
  AMP PEAK  9(6P21.33) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK  9(6P21.33) MUTATED                                              2
  AMP PEAK  9(6P21.33) WILD-TYPE                                            2
D9V6, multiclass
                                               clus
vv                                              AMP PEAK  9(6P21.33) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        41
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              AMP PEAK  9(6P21.33) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         103
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  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"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(6P21.33) MUTATED     8  40
  AMP PEAK  9(6P21.33) WILD-TYPE  19 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(6P21.33) MUTATED      8   40
  AMP PEAK  9(6P21.33) WILD-TYPE   19  109
     clus
vv    AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  NO                             8                             19
  YES                           40                            109
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(6P21.33) MUTATED                                  1     4
  AMP PEAK  9(6P21.33) WILD-TYPE                                6    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(6P21.33) MUTATED                           5
  AMP PEAK  9(6P21.33) WILD-TYPE                        13
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  9(6P21.33) MUTATED                                           1
  AMP PEAK  9(6P21.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK  9(6P21.33) MUTATED      36
  AMP PEAK  9(6P21.33) WILD-TYPE    94
D9V10, multiclass
                                           clus
vv                                          AMP PEAK  9(6P21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               36
                                           clus
vv                                          AMP PEAK  9(6P21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"
D9V11, binary
                                cls
clus                              0  1
  AMP PEAK  9(6P21.33) MUTATED    1 35
  AMP PEAK  9(6P21.33) WILD-TYPE 10 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(6P21.33) MUTATED      1   35
  AMP PEAK  9(6P21.33) WILD-TYPE   10   92
                        clus
vv                       AMP PEAK  9(6P21.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       AMP PEAK  9(6P21.33) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             92
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                                cls
clus                              0  1
  AMP PEAK  9(6P21.33) MUTATED   11  9
  AMP PEAK  9(6P21.33) WILD-TYPE 37 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(6P21.33) MUTATED     11    9
  AMP PEAK  9(6P21.33) WILD-TYPE   37   10
            clus
vv           AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  TUMOR FREE                           11                             37
  WITH TUMOR                            9                             10
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK  9(6P21.33) MUTATED         1      2       2            39       4
  AMP PEAK  9(6P21.33) WILD-TYPE       0      8       4           108       8
D9V14, multiclass
               clus
vv              AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  NIGERIA                                  1                              0
  RUSSIA                                   2                              8
  UKRAINE                                  2                              4
  UNITED STATES                           39                            108
  VIETNAM                                  4                              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK  9(6P21.33) MUTATED    1 21 25  1  0
  AMP PEAK  9(6P21.33) WILD-TYPE 13 62 47  0  5
D9V15, multiclass
    clus
vv   AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  G1                            1                             13
  G2                           21                             62
  G3                           25                             47
  G4                            1                              0
  GX                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V16, continuous
D9V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK  9(6P21.33) MUTATED                                             4
  AMP PEAK  9(6P21.33) WILD-TYPE                                          17
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK  9(6P21.33) MUTATED                                        2
  AMP PEAK  9(6P21.33) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK  9(6P21.33) MUTATED                                                 0
  AMP PEAK  9(6P21.33) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK  9(6P21.33) MUTATED               12                  23
  AMP PEAK  9(6P21.33) WILD-TYPE             24                  60
D9V18, multiclass
                                                 clus
vv                                                AMP PEAK  9(6P21.33) 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                                                            12
  LIFELONG NON-SMOKER                                                       23
                                                 clus
vv                                                AMP PEAK  9(6P21.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              24
  LIFELONG NON-SMOKER                                                         60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK  9(6P21.33) MUTATED             6       11             2        2
  AMP PEAK  9(6P21.33) WILD-TYPE          11       26             9        3
D9V20, multiclass
               clus
vv              AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  COMBINATION                              6                             11
  EXTERNAL                                11                             26
  EXTERNAL BEAM                            2                              9
  INTERNAL                                 2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V21, binary
                                cls
clus                             0 1
  AMP PEAK  9(6P21.33) MUTATED   4 0
  AMP PEAK  9(6P21.33) WILD-TYPE 7 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(6P21.33) MUTATED      4    0
  AMP PEAK  9(6P21.33) WILD-TYPE    7    3
     clus
vv    AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  CGY                            4                              7
  GY                             0                              3
[1] 2 2
[1] FALSE
D9V22, continuous
D9V23, continuous
D9V24, continuous
D9V25, continuous
D9V26, continuous
D9V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  9(6P21.33) MUTATED                                     0
  AMP PEAK  9(6P21.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK  9(6P21.33) MUTATED                                     1
  AMP PEAK  9(6P21.33) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK  9(6P21.33) MUTATED                         2
  AMP PEAK  9(6P21.33) WILD-TYPE                       7
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK  9(6P21.33) MUTATED                         0
  AMP PEAK  9(6P21.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK  9(6P21.33) MUTATED                         1
  AMP PEAK  9(6P21.33) WILD-TYPE                       4
D9V28, multiclass
                                     clus
vv                                    AMP PEAK  9(6P21.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        2
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK  9(6P21.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          7
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  AMP PEAK  9(6P21.33) MUTATED                                               0
  AMP PEAK  9(6P21.33) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK  9(6P21.33) MUTATED                                                3
  AMP PEAK  9(6P21.33) WILD-TYPE                                              7
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK  9(6P21.33) MUTATED                                                                                  12
  AMP PEAK  9(6P21.33) WILD-TYPE                                                                                42
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK  9(6P21.33) MUTATED                                                                                             21
  AMP PEAK  9(6P21.33) WILD-TYPE                                                                                           56
D9V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK  9(6P21.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           21
                                                                                              clus
vv                                                                                             AMP PEAK  9(6P21.33) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V30, binary
                                cls
clus                              0  1
  AMP PEAK  9(6P21.33) MUTATED   11 17
  AMP PEAK  9(6P21.33) WILD-TYPE 43 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(6P21.33) MUTATED     11   17
  AMP PEAK  9(6P21.33) WILD-TYPE   43   42
         clus
vv        AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  ABSENT                            11                             43
  PRESENT                           17                             42
[1] 2 2
[1] FALSE
D9V31, continuous
D9V32, continuous
D9V33, binary
                                cls
clus                              0  1
  AMP PEAK  9(6P21.33) MUTATED    7 21
  AMP PEAK  9(6P21.33) WILD-TYPE 28 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(6P21.33) MUTATED      7   21
  AMP PEAK  9(6P21.33) WILD-TYPE   28   60
                                          clus
vv                                         AMP PEAK  9(6P21.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           21
                                          clus
vv                                         AMP PEAK  9(6P21.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             60
[1] 2 2
[1] FALSE
D9V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK  9(6P21.33) MUTATED       0                   30                   3
  AMP PEAK  9(6P21.33) WILD-TYPE     3                   83                   2
D9V35, multiclass
                      clus
vv                     AMP PEAK  9(6P21.33) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           30
  SIMPLE HYSTERECTOMY                             3
                      clus
vv                     AMP PEAK  9(6P21.33) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             83
  SIMPLE HYSTERECTOMY                               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK  9(6P21.33) MUTATED              0          13          9
  AMP PEAK  9(6P21.33) WILD-TYPE            8          27         31
D9V36, multiclass
              clus
vv             AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  CURRENT USER                            0                              8
  FORMER USER                            13                             27
  NEVER USED                              9                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V37, continuous
D9V38, binary
                                cls
clus                              0  1
  AMP PEAK  9(6P21.33) MUTATED   14  6
  AMP PEAK  9(6P21.33) WILD-TYPE 59  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(6P21.33) MUTATED     14    6
  AMP PEAK  9(6P21.33) WILD-TYPE   59    8
         clus
vv        AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  ABSENT                            14                             59
  PRESENT                            6                              8
[1] 2 2
[1] FALSE
D9V39, continuous
[1] "Remove cluster labels:"       "AMP PEAK  9(6P21.33) MUTATED"
clus
  AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1MN                     TCGA-C5-A1MP 
"AMP PEAK  9(6P21.33) WILD-TYPE" "AMP PEAK  9(6P21.33) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-HM-A3JK 
"AMP PEAK  9(6P21.33) WILD-TYPE" "AMP PEAK  9(6P21.33) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-MU-A51Y 
"AMP PEAK  9(6P21.33) WILD-TYPE" "AMP PEAK  9(6P21.33) WILD-TYPE" 
                    TCGA-MU-A8JM 
"AMP PEAK  9(6P21.33) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK  9(6P21.33) MUTATED     0    1   3   15    6  1   1    3    1   3
  AMP PEAK  9(6P21.33) WILD-TYPE   2    0  19   36   15  2   5    3    7  10
                                vv
clus                             T3B T4 TX
  AMP PEAK  9(6P21.33) MUTATED     1  0  1
  AMP PEAK  9(6P21.33) WILD-TYPE   1  1  6
D9V40, multiclass
      clus
vv     AMP PEAK  9(6P21.33) MUTATED AMP PEAK  9(6P21.33) WILD-TYPE
  T1A                             0                              2
  T1A1                            1                              0
  T1B                             3                             19
  T1B1                           15                             36
  T1B2                            6                             15
  T2                              1                              2
  T2A                             1                              5
  T2A1                            3                              3
  T2A2                            1                              7
  T2B                             3                             10
  T3B                             1                              1
  T4                              0                              1
  TX                              1                              6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V41, continuous

Clustering(10) Variable = AMP PEAK 10(7P11.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P11.2) MUTATED    24   8
  AMP PEAK 10(7P11.2) WILD-TYPE 113  24
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                           32                           137 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                            8                            24 
$`AMP PEAK 10(7P11.2) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BL TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LY 
       11.44       173.29         2.43        40.93        73.18        78.35 
TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UH TCGA-DR-A0ZL TCGA-DS-A0VK 
      100.14        25.35        73.41        60.69        87.75        36.76 
TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A50E TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RB 
       22.98         8.28         0.26        12.59         0.53         0.07 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A40J 
        0.36         1.18         2.24         6.94        23.84         1.35 
TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B 
       21.67        78.71        36.36        19.33        20.48        10.06 
TCGA-Q1-A6DT TCGA-R2-A69V 
        3.39        19.59 

$`AMP PEAK 10(7P11.2) 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-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-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-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
       38.99        35.61         0.46         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       83.05        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93       101.82       134.33        15.48         9.67 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       17.19        85.55        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88         2.66       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 
        7.33         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         0.69        14.99        14.96        13.58        13.48 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL 
       45.96         6.64         0.59         4.04         0.03        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
        7.92        14.70         4.47         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.32         1.97         1.12        25.41 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         4.11       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI 
      117.40        96.95        81.96        26.56        14.43        16.64 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       15.58         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96         3.72         3.45         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25         3.88        11.67        93.99 

  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                       173.29                        182.93 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                       20.035                        13.050 
[1] "0.1 - 173.3 (20.0)" "0.0 - 182.9 (13.1)"
[1] "hr=" "1.2"
D10V2, continuous
                               vv
clus                            T1 T2+T3+T4
  AMP PEAK 10(7P11.2) MUTATED   12        9
  AMP PEAK 10(7P11.2) WILD-TYPE 85       30
D10V3, multiclass
          clus
vv         AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  T1                                12                            85
  T2+T3+T4                           9                            30
[1] 2 2
[1] FALSE
D10V4, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P11.2) MUTATED   10  8
  AMP PEAK 10(7P11.2) WILD-TYPE 77 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED     10    8
  AMP PEAK 10(7P11.2) WILD-TYPE   77   32
   clus
vv  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  0                          10                            77
  1                           8                            32
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 10(7P11.2) MUTATED   11  0 11
  AMP PEAK 10(7P11.2) WILD-TYPE 61  3 54
D10V5, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  M0                          11                            61
  M1                           0                             3
  MX                          11                            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(7P11.2) MUTATED               0                               30
  AMP PEAK 10(7P11.2) WILD-TYPE             2                              114
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 10(7P11.2) MUTATED                                               0
  AMP PEAK 10(7P11.2) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                     2
  AMP PEAK 10(7P11.2) WILD-TYPE                                  18
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 10(7P11.2) MUTATED                                           0
  AMP PEAK 10(7P11.2) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 10(7P11.2) MUTATED                                              0
  AMP PEAK 10(7P11.2) WILD-TYPE                                            4
D10V6, multiclass
                                               clus
vv                                              AMP PEAK 10(7P11.2) 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                                              AMP PEAK 10(7P11.2) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        114
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 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"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED     8  24
  AMP PEAK 10(7P11.2) WILD-TYPE  19 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      8   24
  AMP PEAK 10(7P11.2) WILD-TYPE   19  125
     clus
vv    AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  NO                            8                            19
  YES                          24                           125
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(7P11.2) MUTATED                                  1     2
  AMP PEAK 10(7P11.2) WILD-TYPE                                6    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(7P11.2) MUTATED                           6
  AMP PEAK 10(7P11.2) WILD-TYPE                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(7P11.2) MUTATED                                           0    22
  AMP PEAK 10(7P11.2) WILD-TYPE                                         1   108
D10V10, multiclass
                                           clus
vv                                          AMP PEAK 10(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              22
                                           clus
vv                                          AMP PEAK 10(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               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"
D10V11, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED     2  25
  AMP PEAK 10(7P11.2) WILD-TYPE   9 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      2   25
  AMP PEAK 10(7P11.2) WILD-TYPE    9  102
                        clus
vv                       AMP PEAK 10(7P11.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          25
                        clus
vv                       AMP PEAK 10(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           102
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P11.2) MUTATED    8  7
  AMP PEAK 10(7P11.2) WILD-TYPE 40 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      8    7
  AMP PEAK 10(7P11.2) WILD-TYPE   40   12
            clus
vv           AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  TUMOR FREE                           8                            40
  WITH TUMOR                           7                            12
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 10(7P11.2) MUTATED         0      0       0            31       1
  AMP PEAK 10(7P11.2) WILD-TYPE       1     10       6           116      11
D10V14, multiclass
               clus
vv              AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  0                            10
  UKRAINE                                 0                             6
  UNITED STATES                          31                           116
  VIETNAM                                 1                            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK 10(7P11.2) MUTATED    0 11 18  1  2
  AMP PEAK 10(7P11.2) WILD-TYPE 14 72 54  0  3
D10V15, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  G1                           0                            14
  G2                          11                            72
  G3                          18                            54
  G4                           1                             0
  GX                           2                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V16, continuous
D10V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 10(7P11.2) MUTATED                                             3
  AMP PEAK 10(7P11.2) WILD-TYPE                                          18
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 10(7P11.2) MUTATED                                        3
  AMP PEAK 10(7P11.2) WILD-TYPE                                      5
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 10(7P11.2) MUTATED                                                 0
  AMP PEAK 10(7P11.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 10(7P11.2) MUTATED                4                  16
  AMP PEAK 10(7P11.2) WILD-TYPE             32                  67
D10V18, multiclass
                                                 clus
vv                                                AMP PEAK 10(7P11.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                            4
  LIFELONG NON-SMOKER                                                      16
                                                 clus
vv                                                AMP PEAK 10(7P11.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             32
  LIFELONG NON-SMOKER                                                        67
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 10(7P11.2) MUTATED             4        7             5        2
  AMP PEAK 10(7P11.2) WILD-TYPE          13       30             6        3
D10V20, multiclass
               clus
vv              AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  COMBINATION                             4                            13
  EXTERNAL                                7                            30
  EXTERNAL BEAM                           5                             6
  INTERNAL                                2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V21, binary
                               cls
clus                            0 1
  AMP PEAK 10(7P11.2) MUTATED   6 1
  AMP PEAK 10(7P11.2) WILD-TYPE 5 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      6    1
  AMP PEAK 10(7P11.2) WILD-TYPE    5    2
     clus
vv    AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  CGY                           6                             5
  GY                            1                             2
[1] 2 2
[1] FALSE
D10V22, continuous
D10V23, continuous
D10V24, continuous
D10V25, continuous
D10V26, continuous
D10V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 10(7P11.2) MUTATED                                     0
  AMP PEAK 10(7P11.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 10(7P11.2) MUTATED                                     1
  AMP PEAK 10(7P11.2) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 10(7P11.2) MUTATED                         1                       1
  AMP PEAK 10(7P11.2) WILD-TYPE                       8                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK 10(7P11.2) MUTATED                         2
  AMP PEAK 10(7P11.2) WILD-TYPE                       3
D10V28, multiclass
                                     clus
vv                                    AMP PEAK 10(7P11.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                       1
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    AMP PEAK 10(7P11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                         8
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         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)
  AMP PEAK 10(7P11.2) MUTATED                                               0
  AMP PEAK 10(7P11.2) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 10(7P11.2) MUTATED                                                1
  AMP PEAK 10(7P11.2) WILD-TYPE                                              9
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 10(7P11.2) MUTATED                                                                                  10
  AMP PEAK 10(7P11.2) WILD-TYPE                                                                                44
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 10(7P11.2) MUTATED                                                                                             16
  AMP PEAK 10(7P11.2) WILD-TYPE                                                                                           61
D10V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 10(7P11.2) 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)                          16
                                                                                              clus
vv                                                                                             AMP PEAK 10(7P11.2) 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)                                       44
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V30, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P11.2) MUTATED    6 13
  AMP PEAK 10(7P11.2) WILD-TYPE 48 46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      6   13
  AMP PEAK 10(7P11.2) WILD-TYPE   48   46
         clus
vv        AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  ABSENT                            6                            48
  PRESENT                          13                            46
[1] 2 2
[1] FALSE
D10V31, continuous
D10V32, continuous
D10V33, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P11.2) MUTATED    8 14
  AMP PEAK 10(7P11.2) WILD-TYPE 27 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      8   14
  AMP PEAK 10(7P11.2) WILD-TYPE   27   67
                                          clus
vv                                         AMP PEAK 10(7P11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          14
                                          clus
vv                                         AMP PEAK 10(7P11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            67
[1] 2 2
[1] FALSE
D10V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 10(7P11.2) MUTATED       0                   15                   0
  AMP PEAK 10(7P11.2) WILD-TYPE     3                   98                   5
D10V35, multiclass
                      clus
vv                     AMP PEAK 10(7P11.2) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          15
  SIMPLE HYSTERECTOMY                            0
                      clus
vv                     AMP PEAK 10(7P11.2) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            98
  SIMPLE HYSTERECTOMY                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK 10(7P11.2) MUTATED              2           7          7
  AMP PEAK 10(7P11.2) WILD-TYPE            6          33         33
D10V36, multiclass
              clus
vv             AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  CURRENT USER                           2                             6
  FORMER USER                            7                            33
  NEVER USED                             7                            33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V37, continuous
D10V38, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P11.2) MUTATED   12  2
  AMP PEAK 10(7P11.2) WILD-TYPE 61 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED     12    2
  AMP PEAK 10(7P11.2) WILD-TYPE   61   12
         clus
vv        AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  ABSENT                           12                            61
  PRESENT                           2                            12
[1] 2 2
[1] FALSE
D10V39, continuous
[1] "Remove cluster labels:"      "AMP PEAK 10(7P11.2) MUTATED"
clus
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                            1                             8 
                   TCGA-C5-A1BN                    TCGA-C5-A1MH 
"AMP PEAK 10(7P11.2) WILD-TYPE" "AMP PEAK 10(7P11.2) WILD-TYPE" 
                   TCGA-C5-A1MP                    TCGA-EK-A2RO 
"AMP PEAK 10(7P11.2) WILD-TYPE" "AMP PEAK 10(7P11.2) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-JW-A852 
"AMP PEAK 10(7P11.2) WILD-TYPE" "AMP PEAK 10(7P11.2) WILD-TYPE" 
                   TCGA-MU-A51Y                    TCGA-MU-A8JM 
"AMP PEAK 10(7P11.2) WILD-TYPE" "AMP PEAK 10(7P11.2) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK 10(7P11.2) MUTATED     0    0   4    5    3  0   0    4    2   1   1
  AMP PEAK 10(7P11.2) WILD-TYPE   2    1  18   46   18  3   6    2    6  12   1
                               vv
clus                            T4 TX
  AMP PEAK 10(7P11.2) MUTATED    1  1
  AMP PEAK 10(7P11.2) WILD-TYPE  0  6
D10V40, multiclass
      clus
vv     AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  T1A                            0                             2
  T1A1                           0                             1
  T1B                            4                            18
  T1B1                           5                            46
  T1B2                           3                            18
  T2                             0                             3
  T2A                            0                             6
  T2A1                           4                             2
  T2A2                           2                             6
  T2B                            1                            12
  T3B                            1                             1
  T4                             1                             0
  TX                             1                             6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V41, continuous

Clustering(11) Variable = AMP PEAK 11(8Q24.21) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(8Q24.21) MUTATED   55 14
  AMP PEAK 11(8Q24.21) WILD-TYPE 82 18
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            69                            100 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            14                             18 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
       57.04       177.04        82.85        19.86        67.46        31.40 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP 
       35.01        53.16        38.99        35.61         2.43         3.58 
TCGA-C5-A2LV TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       73.45       100.14        38.43        52.01        18.02        17.85 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DS-A0VL 
      182.93        25.35        60.69        13.61        87.75         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3QD TCGA-EA-A3Y4 
      117.99        22.98        12.36         1.74        13.05        14.50 
TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EK-A2H0 
        1.35        12.82         0.26        14.89        13.91        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        6.64         0.53         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI 
        0.03         6.12         1.22        23.84         0.66         1.45 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LK 
        3.52         1.35         1.32         4.11       137.16        26.56 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       36.36        19.33        15.58         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A5YI TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        0.07         0.82         0.03         4.34         3.45         3.39 
TCGA-Q1-A6DW TCGA-R2-A69V TCGA-RA-A741 
        5.75        19.59         3.88 

$`AMP PEAK 11(8Q24.21) 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-A1BL TCGA-C5-A1BN TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
      144.16       173.29         5.46        46.32        30.21        57.73 
TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY 
        0.46        40.93        44.22        73.18        83.05        78.35 
TCGA-C5-A2M2 TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
        0.82        20.42       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
       73.41        17.19        85.55        94.95         9.34         2.73 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       58.88        36.76       118.65        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
        8.28         0.76         1.32         0.82         0.62         1.18 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A5ZD 
        1.35        14.50         1.81        12.66         1.48         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2R7 
       14.99        14.96        13.58        13.48        12.59         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        2.24        20.35         7.92         6.94        14.70         4.47 
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-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      147.39        66.81       117.40        96.95        78.71        81.96 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B TCGA-MU-A51Y TCGA-MU-A8JM 
       14.43        16.64        20.48        10.06        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         3.72         5.85         3.72 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        11.67        93.99 

  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                        182.93                         173.29 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                        13.050                         13.725 
[1] "0.0 - 182.9 (13.1)" "0.0 - 173.3 (13.7)"
[1] "hr=" "1.2"
D11V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK 11(8Q24.21) MUTATED   39       13
  AMP PEAK 11(8Q24.21) WILD-TYPE 58       26
D11V3, multiclass
          clus
vv         AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  T1                                 39                             58
  T2+T3+T4                           13                             26
[1] 2 2
[1] FALSE
D11V4, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED   33 16
  AMP PEAK 11(8Q24.21) WILD-TYPE 54 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     33   16
  AMP PEAK 11(8Q24.21) WILD-TYPE   54   24
   clus
vv  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  0                           33                             54
  1                           16                             24
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 11(8Q24.21) MUTATED   27  1 26
  AMP PEAK 11(8Q24.21) WILD-TYPE 45  2 39
D11V5, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  M0                           27                             45
  M1                            1                              2
  MX                           26                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(8Q24.21) MUTATED               1                               62
  AMP PEAK 11(8Q24.21) WILD-TYPE             1                               82
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 11(8Q24.21) MUTATED                                               0
  AMP PEAK 11(8Q24.21) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 11(8Q24.21) MUTATED                                     6
  AMP PEAK 11(8Q24.21) WILD-TYPE                                  14
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 11(8Q24.21) MUTATED                                           2
  AMP PEAK 11(8Q24.21) WILD-TYPE                                         0
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 11(8Q24.21) MUTATED                                              1
  AMP PEAK 11(8Q24.21) WILD-TYPE                                            3
D11V6, multiclass
                                               clus
vv                                              AMP PEAK 11(8Q24.21) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        62
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 11(8Q24.21) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                          82
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED    9 63
  AMP PEAK 11(8Q24.21) WILD-TYPE 18 86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED      9   63
  AMP PEAK 11(8Q24.21) WILD-TYPE   18   86
     clus
vv    AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  NO                             9                             18
  YES                           63                             86
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(8Q24.21) MUTATED                                  3     6
  AMP PEAK 11(8Q24.21) WILD-TYPE                                4     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(8Q24.21) MUTATED                           8
  AMP PEAK 11(8Q24.21) WILD-TYPE                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 11(8Q24.21) MUTATED                                           1
  AMP PEAK 11(8Q24.21) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 11(8Q24.21) MUTATED      53
  AMP PEAK 11(8Q24.21) WILD-TYPE    77
D11V10, multiclass
                                           clus
vv                                          AMP PEAK 11(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               53
                                           clus
vv                                          AMP PEAK 11(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED    4 52
  AMP PEAK 11(8Q24.21) WILD-TYPE  7 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED      4   52
  AMP PEAK 11(8Q24.21) WILD-TYPE    7   75
                        clus
vv                       AMP PEAK 11(8Q24.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       AMP PEAK 11(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             75
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED   22 11
  AMP PEAK 11(8Q24.21) WILD-TYPE 26  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     22   11
  AMP PEAK 11(8Q24.21) WILD-TYPE   26    8
            clus
vv           AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  TUMOR FREE                           22                             26
  WITH TUMOR                           11                              8
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 11(8Q24.21) MUTATED         0      4       3            60       5
  AMP PEAK 11(8Q24.21) WILD-TYPE       1      6       3            87       7
D11V14, multiclass
               clus
vv              AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   4                              6
  UKRAINE                                  3                              3
  UNITED STATES                           60                             87
  VIETNAM                                  5                              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 11(8Q24.21) MUTATED    5 26 38  0  3
  AMP PEAK 11(8Q24.21) WILD-TYPE  9 57 34  1  2
D11V15, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  G1                            5                              9
  G2                           26                             57
  G3                           38                             34
  G4                            0                              1
  GX                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V16, continuous
D11V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 11(8Q24.21) MUTATED                                             7
  AMP PEAK 11(8Q24.21) WILD-TYPE                                          14
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 11(8Q24.21) MUTATED                                        3
  AMP PEAK 11(8Q24.21) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 11(8Q24.21) MUTATED                                                 0
  AMP PEAK 11(8Q24.21) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 11(8Q24.21) MUTATED               10                  40
  AMP PEAK 11(8Q24.21) WILD-TYPE             26                  43
D11V18, multiclass
                                                 clus
vv                                                AMP PEAK 11(8Q24.21) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                            10
  LIFELONG NON-SMOKER                                                       40
                                                 clus
vv                                                AMP PEAK 11(8Q24.21) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              26
  LIFELONG NON-SMOKER                                                         43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 11(8Q24.21) MUTATED             8       15             2        2
  AMP PEAK 11(8Q24.21) WILD-TYPE           9       22             9        3
D11V20, multiclass
               clus
vv              AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  COMBINATION                              8                              9
  EXTERNAL                                15                             22
  EXTERNAL BEAM                            2                              9
  INTERNAL                                 2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V21, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED    1  2
  AMP PEAK 11(8Q24.21) WILD-TYPE 10  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED      1    2
  AMP PEAK 11(8Q24.21) WILD-TYPE   10    1
     clus
vv    AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  CGY                            1                             10
  GY                             2                              1
[1] 2 2
[1] FALSE
D11V22, continuous
D11V23, continuous
D11V24, continuous
D11V25, continuous
D11V26, continuous
D11V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 11(8Q24.21) MUTATED                                     1
  AMP PEAK 11(8Q24.21) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 11(8Q24.21) MUTATED                                     1
  AMP PEAK 11(8Q24.21) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 11(8Q24.21) MUTATED                         4
  AMP PEAK 11(8Q24.21) WILD-TYPE                       5
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 11(8Q24.21) MUTATED                         1
  AMP PEAK 11(8Q24.21) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 11(8Q24.21) MUTATED                         1
  AMP PEAK 11(8Q24.21) WILD-TYPE                       4
D11V28, multiclass
                                     clus
vv                                    AMP PEAK 11(8Q24.21) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        4
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 11(8Q24.21) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          5
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          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)
  AMP PEAK 11(8Q24.21) MUTATED                                               1
  AMP PEAK 11(8Q24.21) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 11(8Q24.21) MUTATED                                                4
  AMP PEAK 11(8Q24.21) WILD-TYPE                                              6
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 11(8Q24.21) MUTATED                                                                                  27
  AMP PEAK 11(8Q24.21) WILD-TYPE                                                                                27
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 11(8Q24.21) MUTATED                                                                                             29
  AMP PEAK 11(8Q24.21) WILD-TYPE                                                                                           48
D11V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 11(8Q24.21) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           29
                                                                                              clus
vv                                                                                             AMP PEAK 11(8Q24.21) 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)                                        27
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V30, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED   19 22
  AMP PEAK 11(8Q24.21) WILD-TYPE 35 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     19   22
  AMP PEAK 11(8Q24.21) WILD-TYPE   35   37
         clus
vv        AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  ABSENT                            19                             35
  PRESENT                           22                             37
[1] 2 2
[1] FALSE
D11V31, continuous
D11V32, continuous
D11V33, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED   16 34
  AMP PEAK 11(8Q24.21) WILD-TYPE 19 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     16   34
  AMP PEAK 11(8Q24.21) WILD-TYPE   19   47
                                          clus
vv                                         AMP PEAK 11(8Q24.21) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           34
                                          clus
vv                                         AMP PEAK 11(8Q24.21) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             47
[1] 2 2
[1] FALSE
D11V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 11(8Q24.21) MUTATED       1                   44                   4
  AMP PEAK 11(8Q24.21) WILD-TYPE     2                   69                   1
D11V35, multiclass
                      clus
vv                     AMP PEAK 11(8Q24.21) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           44
  SIMPLE HYSTERECTOMY                             4
                      clus
vv                     AMP PEAK 11(8Q24.21) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             69
  SIMPLE HYSTERECTOMY                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 11(8Q24.21) MUTATED              1          16         14
  AMP PEAK 11(8Q24.21) WILD-TYPE            7          24         26
D11V36, multiclass
              clus
vv             AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  CURRENT USER                            1                              7
  FORMER USER                            16                             24
  NEVER USED                             14                             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V37, continuous
D11V38, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED   28  3
  AMP PEAK 11(8Q24.21) WILD-TYPE 45 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     28    3
  AMP PEAK 11(8Q24.21) WILD-TYPE   45   11
         clus
vv        AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  ABSENT                            28                             45
  PRESENT                            3                             11
[1] 2 2
[1] FALSE
D11V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 11(8Q24.21) MUTATED     2    1   7   19   10  2   2    2    1   3
  AMP PEAK 11(8Q24.21) WILD-TYPE   0    0  15   32   11  1   4    4    7  10
                                vv
clus                             T3B T4 TX
  AMP PEAK 11(8Q24.21) MUTATED     2  1  4
  AMP PEAK 11(8Q24.21) WILD-TYPE   0  0  3
D11V40, multiclass
      clus
vv     AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  T1A                             2                              0
  T1A1                            1                              0
  T1B                             7                             15
  T1B1                           19                             32
  T1B2                           10                             11
  T2                              2                              1
  T2A                             2                              4
  T2A1                            2                              4
  T2A2                            1                              7
  T2B                             3                             10
  T3B                             2                              0
  T4                              1                              0
  TX                              4                              3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V41, continuous

Clustering(12) Variable = AMP PEAK 12(9P24.1) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(9P24.1) MUTATED    33   3
  AMP PEAK 12(9P24.1) WILD-TYPE 104  29
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                           36                           133 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                            3                            29 
$`AMP PEAK 12(9P24.1) MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       49.48       177.04         3.58        73.18        73.45        83.05 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO 
        0.82        52.01       182.93       134.33        15.48        73.41 
TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A3QD 
       85.55         2.73       117.99        22.98        16.83        13.05 
TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EK-A2PG TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A3L1 
       13.91        14.99         0.53         2.24         0.10         6.94 
TCGA-FU-A23K TCGA-FU-A40J TCGA-IR-A3LH TCGA-IR-A3LL TCGA-JW-A5VL TCGA-JW-A69B 
        1.22         1.35        78.71        36.36        15.58        10.06 
TCGA-LP-A4AU TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD TCGA-UC-A7PF 
        0.10         0.07         2.96         3.45        11.67        93.99 

$`AMP PEAK 12(9P24.1) 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-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       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-A2LS 
       38.99        35.61         0.46         2.43        40.93        44.22 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14        38.43        18.02        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI 
       25.35       101.82         9.67        17.19        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        9.34        13.61        87.75        58.88        36.76         2.66 
TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
      118.65        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.74         1.32         0.82         0.62         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-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-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX 
        0.26        14.89         1.48         0.69        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB 
       13.48        12.59        45.96         6.64         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-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-A449 
        0.10         0.10         0.03        20.35         7.92        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.47         6.12        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-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       96.95        81.96        26.56        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
       20.48         5.13         0.89         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
        0.03         5.42        29.72         4.34         3.72         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 
        3.88 

  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                       182.93                        173.29 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                       15.235                        12.820 
[1] "0.1 - 182.9 (15.2)" "0.0 - 173.3 (12.8)"
[1] "hr=" "3.9"
D12V2, continuous
                               vv
clus                            T1 T2+T3+T4
  AMP PEAK 12(9P24.1) MUTATED   17       10
  AMP PEAK 12(9P24.1) WILD-TYPE 80       29
D12V3, multiclass
          clus
vv         AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  T1                                17                            80
  T2+T3+T4                          10                            29
[1] 2 2
[1] FALSE
D12V4, binary
                               cls
clus                             0  1
  AMP PEAK 12(9P24.1) MUTATED   12 13
  AMP PEAK 12(9P24.1) WILD-TYPE 75 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED     12   13
  AMP PEAK 12(9P24.1) WILD-TYPE   75   27
   clus
vv  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  0                          12                            75
  1                          13                            27
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 12(9P24.1) MUTATED   15  0 13
  AMP PEAK 12(9P24.1) WILD-TYPE 57  3 52
D12V5, multiclass
    clus
vv   AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  M0                          15                            57
  M1                           0                             3
  MX                          13                            52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(9P24.1) MUTATED               0                               33
  AMP PEAK 12(9P24.1) WILD-TYPE             2                              111
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 12(9P24.1) MUTATED                                               0
  AMP PEAK 12(9P24.1) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 12(9P24.1) MUTATED                                     3
  AMP PEAK 12(9P24.1) WILD-TYPE                                  17
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 12(9P24.1) MUTATED                                           0
  AMP PEAK 12(9P24.1) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 12(9P24.1) MUTATED                                              1
  AMP PEAK 12(9P24.1) WILD-TYPE                                            3
D12V6, multiclass
                                               clus
vv                                              AMP PEAK 12(9P24.1) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       33
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              AMP PEAK 12(9P24.1) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        111
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(9P24.1) MUTATED     3  34
  AMP PEAK 12(9P24.1) WILD-TYPE  24 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED      3   34
  AMP PEAK 12(9P24.1) WILD-TYPE   24  115
     clus
vv    AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  NO                            3                            24
  YES                          34                           115
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(9P24.1) MUTATED                                  2     2
  AMP PEAK 12(9P24.1) WILD-TYPE                                5    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(9P24.1) MUTATED                           7
  AMP PEAK 12(9P24.1) WILD-TYPE                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(9P24.1) MUTATED                                           0    24
  AMP PEAK 12(9P24.1) WILD-TYPE                                         1   106
D12V10, multiclass
                                           clus
vv                                          AMP PEAK 12(9P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              24
                                           clus
vv                                          AMP PEAK 12(9P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               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"
D12V11, binary
                               cls
clus                              0   1
  AMP PEAK 12(9P24.1) MUTATED     2  24
  AMP PEAK 12(9P24.1) WILD-TYPE   9 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED      2   24
  AMP PEAK 12(9P24.1) WILD-TYPE    9  103
                        clus
vv                       AMP PEAK 12(9P24.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          24
                        clus
vv                       AMP PEAK 12(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           103
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                               cls
clus                             0  1
  AMP PEAK 12(9P24.1) MUTATED   14  0
  AMP PEAK 12(9P24.1) WILD-TYPE 34 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED     14    0
  AMP PEAK 12(9P24.1) WILD-TYPE   34   19
            clus
vv           AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  TUMOR FREE                          14                            34
  WITH TUMOR                           0                            19
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 12(9P24.1) MUTATED         1      0       1            33       2
  AMP PEAK 12(9P24.1) WILD-TYPE       0     10       5           114      10
D12V14, multiclass
               clus
vv              AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  NIGERIA                                 1                             0
  RUSSIA                                  0                            10
  UKRAINE                                 1                             5
  UNITED STATES                          33                           114
  VIETNAM                                 2                            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  AMP PEAK 12(9P24.1) MUTATED    1 16 18  1  1
  AMP PEAK 12(9P24.1) WILD-TYPE 13 67 54  0  4
D12V15, multiclass
    clus
vv   AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  G1                           1                            13
  G2                          16                            67
  G3                          18                            54
  G4                           1                             0
  GX                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V16, continuous
D12V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 12(9P24.1) MUTATED                                             4
  AMP PEAK 12(9P24.1) WILD-TYPE                                          17
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 12(9P24.1) MUTATED                                        2
  AMP PEAK 12(9P24.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 12(9P24.1) MUTATED                                                 1
  AMP PEAK 12(9P24.1) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 12(9P24.1) MUTATED                9                  16
  AMP PEAK 12(9P24.1) WILD-TYPE             27                  67
D12V18, multiclass
                                                 clus
vv                                                AMP PEAK 12(9P24.1) 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                                                            9
  LIFELONG NON-SMOKER                                                      16
                                                 clus
vv                                                AMP PEAK 12(9P24.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             27
  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"
D12V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 12(9P24.1) MUTATED             1       11             2        3
  AMP PEAK 12(9P24.1) WILD-TYPE          16       26             9        2
D12V20, multiclass
               clus
vv              AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  COMBINATION                             1                            16
  EXTERNAL                               11                            26
  EXTERNAL BEAM                           2                             9
  INTERNAL                                3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V21, binary
                               cls
clus                            0 1
  AMP PEAK 12(9P24.1) MUTATED   3 1
  AMP PEAK 12(9P24.1) WILD-TYPE 8 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED      3    1
  AMP PEAK 12(9P24.1) WILD-TYPE    8    2
     clus
vv    AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  CGY                           3                             8
  GY                            1                             2
[1] 2 2
[1] FALSE
D12V22, continuous
D12V23, continuous
D12V24, continuous
D12V25, continuous
D12V26, continuous
D12V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 12(9P24.1) MUTATED                                     0
  AMP PEAK 12(9P24.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 12(9P24.1) MUTATED                                     0
  AMP PEAK 12(9P24.1) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 12(9P24.1) MUTATED                         4                       0
  AMP PEAK 12(9P24.1) WILD-TYPE                       5                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  AMP PEAK 12(9P24.1) MUTATED                         2
  AMP PEAK 12(9P24.1) WILD-TYPE                       3
D12V28, multiclass
                                     clus
vv                                    AMP PEAK 12(9P24.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       4
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    AMP PEAK 12(9P24.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                         5
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  AMP PEAK 12(9P24.1) MUTATED                                               0
  AMP PEAK 12(9P24.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 12(9P24.1) MUTATED                                                1
  AMP PEAK 12(9P24.1) WILD-TYPE                                              9
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 12(9P24.1) MUTATED                                                                                  12
  AMP PEAK 12(9P24.1) WILD-TYPE                                                                                42
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 12(9P24.1) MUTATED                                                                                             16
  AMP PEAK 12(9P24.1) WILD-TYPE                                                                                           61
D12V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 12(9P24.1) 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)                          16
                                                                                              clus
vv                                                                                             AMP PEAK 12(9P24.1) 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)                                       42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V30, binary
                               cls
clus                             0  1
  AMP PEAK 12(9P24.1) MUTATED    8 15
  AMP PEAK 12(9P24.1) WILD-TYPE 46 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED      8   15
  AMP PEAK 12(9P24.1) WILD-TYPE   46   44
         clus
vv        AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  ABSENT                            8                            46
  PRESENT                          15                            44
[1] 2 2
[1] FALSE
D12V31, continuous
D12V32, continuous
D12V33, binary
                               cls
clus                             0  1
  AMP PEAK 12(9P24.1) MUTATED    9 13
  AMP PEAK 12(9P24.1) WILD-TYPE 26 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED      9   13
  AMP PEAK 12(9P24.1) WILD-TYPE   26   68
                                          clus
vv                                         AMP PEAK 12(9P24.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          13
                                          clus
vv                                         AMP PEAK 12(9P24.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            68
[1] 2 2
[1] FALSE
D12V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 12(9P24.1) MUTATED       0                   23                   1
  AMP PEAK 12(9P24.1) WILD-TYPE     3                   90                   4
D12V35, multiclass
                      clus
vv                     AMP PEAK 12(9P24.1) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          23
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     AMP PEAK 12(9P24.1) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            90
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  AMP PEAK 12(9P24.1) MUTATED              2          11          4
  AMP PEAK 12(9P24.1) WILD-TYPE            6          29         36
D12V36, multiclass
              clus
vv             AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  CURRENT USER                           2                             6
  FORMER USER                           11                            29
  NEVER USED                             4                            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V37, continuous
D12V38, binary
                               cls
clus                             0  1
  AMP PEAK 12(9P24.1) MUTATED   12  2
  AMP PEAK 12(9P24.1) WILD-TYPE 61 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED     12    2
  AMP PEAK 12(9P24.1) WILD-TYPE   61   12
         clus
vv        AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  ABSENT                           12                            61
  PRESENT                           2                            12
[1] 2 2
[1] FALSE
D12V39, continuous
[1] "Remove cluster labels:"      "AMP PEAK 12(9P24.1) MUTATED"
clus
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                            1                             8 
                   TCGA-C5-A1BN                    TCGA-C5-A1MH 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-C5-A1MN                    TCGA-EK-A2RO 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-JW-A852 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-MU-A51Y                    TCGA-MU-A8JM 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK 12(9P24.1) MUTATED     0    0   5    8    4  2   1    3    0   3   1
  AMP PEAK 12(9P24.1) WILD-TYPE   2    1  17   43   17  1   5    3    8  10   1
                               vv
clus                            T4 TX
  AMP PEAK 12(9P24.1) MUTATED    0  1
  AMP PEAK 12(9P24.1) WILD-TYPE  1  6
D12V40, multiclass
      clus
vv     AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  T1A                            0                             2
  T1A1                           0                             1
  T1B                            5                            17
  T1B1                           8                            43
  T1B2                           4                            17
  T2                             2                             1
  T2A                            1                             5
  T2A1                           3                             3
  T2A2                           0                             8
  T2B                            3                            10
  T3B                            1                             1
  T4                             0                             1
  TX                             1                             6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V41, continuous

Clustering(13) Variable = AMP PEAK 13(11P13) MUTATION ANALYSIS
D13V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 13(11P13) MUTATED     9   4
  AMP PEAK 13(11P13) WILD-TYPE 128  28
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          13                          156 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                           4                           28 
$`AMP PEAK 13(11P13) MUTATED`
TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-EA-A439 TCGA-EA-A78R 
        5.46        31.40        35.01        73.18        14.50        13.48 
TCGA-EK-A2H0 TCGA-FU-A40J TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-PN-A8MA 
       45.96         1.35        26.56        16.64        19.33         2.96 
TCGA-Q1-A6DW 
        5.75 

$`AMP PEAK 13(11P13) 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-A1BQ 
       36.56       144.16       177.04       173.29        82.85        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-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-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       182.93        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       85.55        60.69        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       12.36         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-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         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG 
       14.99        14.96        13.58        12.59         6.64         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-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         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VK 
       96.95        78.71        81.96        36.36        14.43        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        4.34         3.72         3.45         5.85         3.39         3.72 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                        1.35                         0.03 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                       73.18                       182.93 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                      16.640                       12.935 
[1] "1.4 - 73.2 (16.6)"  "0.0 - 182.9 (12.9)"
[1] "hr=" "2.1"
D13V2, continuous
                              vv
clus                           T1 T2+T3+T4
  AMP PEAK 13(11P13) MUTATED    3        6
  AMP PEAK 13(11P13) WILD-TYPE 94       33
D13V3, multiclass
          clus
vv         AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  T1                                3                           94
  T2+T3+T4                          6                           33
[1] 2 2
[1] FALSE
D13V4, binary
                              cls
clus                            0  1
  AMP PEAK 13(11P13) MUTATED    4  2
  AMP PEAK 13(11P13) WILD-TYPE 83 38
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      4    2
  AMP PEAK 13(11P13) WILD-TYPE   83   38
   clus
vv  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  0                          4                           83
  1                          2                           38
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  AMP PEAK 13(11P13) MUTATED    6  0  4
  AMP PEAK 13(11P13) WILD-TYPE 66  3 61
D13V5, multiclass
    clus
vv   AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  M0                          6                           66
  M1                          0                            3
  MX                          4                           61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(11P13) MUTATED               0                               12
  AMP PEAK 13(11P13) WILD-TYPE             2                              132
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 13(11P13) MUTATED                                               0
  AMP PEAK 13(11P13) WILD-TYPE                                             4
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 13(11P13) MUTATED                                     2
  AMP PEAK 13(11P13) WILD-TYPE                                  18
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 13(11P13) MUTATED                                           0
  AMP PEAK 13(11P13) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 13(11P13) MUTATED                                              0
  AMP PEAK 13(11P13) WILD-TYPE                                            4
D13V6, multiclass
                                               clus
vv                                              AMP PEAK 13(11P13) MUTATED
  ADENOSQUAMOUS                                                          0
  CERVICAL SQUAMOUS CELL CARCINOMA                                      12
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           0
                                               clus
vv                                              AMP PEAK 13(11P13) WILD-TYPE
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       132
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED     4  10
  AMP PEAK 13(11P13) WILD-TYPE  23 139
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      4   10
  AMP PEAK 13(11P13) WILD-TYPE   23  139
     clus
vv    AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  NO                           4                           23
  YES                         10                          139
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(11P13) MUTATED                                  2     2
  AMP PEAK 13(11P13) WILD-TYPE                                5    13
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(11P13) MUTATED                           1
  AMP PEAK 13(11P13) WILD-TYPE                        17
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(11P13) MUTATED                                           0     9
  AMP PEAK 13(11P13) WILD-TYPE                                         1   121
D13V10, multiclass
                                           clus
vv                                          AMP PEAK 13(11P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                          1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                              9
                                           clus
vv                                          AMP PEAK 13(11P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                               13
  BLACK OR AFRICAN AMERICAN                                           17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              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"
D13V11, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED     2   8
  AMP PEAK 13(11P13) WILD-TYPE   9 119
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      2    8
  AMP PEAK 13(11P13) WILD-TYPE    9  119
                        clus
vv                       AMP PEAK 13(11P13) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                          8
                        clus
vv                       AMP PEAK 13(11P13) WILD-TYPE
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          119
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                              cls
clus                            0  1
  AMP PEAK 13(11P13) MUTATED    3  5
  AMP PEAK 13(11P13) WILD-TYPE 45 14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      3    5
  AMP PEAK 13(11P13) WILD-TYPE   45   14
            clus
vv           AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  TUMOR FREE                          3                           45
  WITH TUMOR                          5                           14
[1] 2 2
[1] FALSE
                              vv
clus                           NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 13(11P13) MUTATED         1      0       0            11       2
  AMP PEAK 13(11P13) WILD-TYPE       0     10       6           136      10
D13V14, multiclass
               clus
vv              AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  NIGERIA                                1                            0
  RUSSIA                                 0                           10
  UKRAINE                                0                            6
  UNITED STATES                         11                          136
  VIETNAM                                2                           10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           G1 G2 G3 G4 GX
  AMP PEAK 13(11P13) MUTATED    0  2 11  0  1
  AMP PEAK 13(11P13) WILD-TYPE 14 81 61  1  4
D13V15, multiclass
    clus
vv   AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  G1                          0                           14
  G2                          2                           81
  G3                         11                           61
  G4                          0                            1
  GX                          1                            4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V16, continuous
[1] "Remove cluster labels:"     "AMP PEAK 13(11P13) MUTATED"
clus
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                           1                           24 
                  TCGA-BI-A0VR                   TCGA-C5-A1BJ 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-C5-A1BL                   TCGA-C5-A1BQ 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-C5-A1ME                   TCGA-C5-A1MF 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-C5-A1MH                   TCGA-C5-A2M2 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-C5-A3HD                   TCGA-C5-A7CM 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-C5-A7CO                   TCGA-DS-A3LQ 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-EX-A69M                   TCGA-FU-A2QG 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-FU-A3TX                   TCGA-FU-A3WB 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-HM-A3JK                   TCGA-HM-A4S6 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-IR-A3L7                   TCGA-IR-A3LB 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-IR-A3LH                   TCGA-MU-A5YI 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-MU-A8JM                   TCGA-RA-A741 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
D13V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 13(11P13) MUTATED                                             1
  AMP PEAK 13(11P13) WILD-TYPE                                          20
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 13(11P13) MUTATED                                        0
  AMP PEAK 13(11P13) WILD-TYPE                                      8
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 13(11P13) MUTATED                                                 0
  AMP PEAK 13(11P13) WILD-TYPE                                               1
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 13(11P13) MUTATED                3                   7
  AMP PEAK 13(11P13) WILD-TYPE             33                  76
D13V18, multiclass
                                                 clus
vv                                                AMP PEAK 13(11P13) 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                                                      7
                                                 clus
vv                                                AMP PEAK 13(11P13) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            33
  LIFELONG NON-SMOKER                                                       76
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V19, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 13(11P13) MUTATED             2        3             2        0
  AMP PEAK 13(11P13) WILD-TYPE          15       34             9        5
D13V20, multiclass
               clus
vv              AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  COMBINATION                            2                           15
  EXTERNAL                               3                           34
  EXTERNAL BEAM                          2                            9
  INTERNAL                               0                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V21, binary
                              cls
clus                            0  1
  AMP PEAK 13(11P13) MUTATED    0  0
  AMP PEAK 13(11P13) WILD-TYPE 11  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      0    0
  AMP PEAK 13(11P13) WILD-TYPE   11    3
D13V22, continuous
D13V23, continuous
D13V24, continuous
D13V25, continuous
D13V26, continuous
D13V27, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 13(11P13) MUTATED                                     0
  AMP PEAK 13(11P13) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 13(11P13) MUTATED                                     1
  AMP PEAK 13(11P13) WILD-TYPE                                   5
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 13(11P13) MUTATED                         0                       0
  AMP PEAK 13(11P13) WILD-TYPE                       9                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 13(11P13) MUTATED                         0
  AMP PEAK 13(11P13) WILD-TYPE                       5
D13V28, multiclass
[1] "Remove cluster labels:"     "AMP PEAK 13(11P13) MUTATED"
clus
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                           1                           22 
                  TCGA-BI-A20A                   TCGA-C5-A0TN 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-C5-A1BE                   TCGA-C5-A1BM 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-C5-A2LX                   TCGA-DR-A0ZM 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-DS-A0VK                   TCGA-DS-A0VL 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-DS-A0VM                   TCGA-DS-A0VN 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-DS-A3LQ                   TCGA-EA-A50E 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-EK-A2RN                   TCGA-EK-A2RO 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-EX-A1H5                   TCGA-EX-A449 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-FU-A3EO                   TCGA-HM-A4S6 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-IR-A3LH                   TCGA-IR-A3LI 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-MU-A8JM                   TCGA-UC-A7PD 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 13(11P13) MUTATED                                               0
  AMP PEAK 13(11P13) WILD-TYPE                                             2
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 13(11P13) MUTATED                                                1
  AMP PEAK 13(11P13) WILD-TYPE                                              9
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 13(11P13) MUTATED                                                                                   3
  AMP PEAK 13(11P13) WILD-TYPE                                                                                51
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 13(11P13) MUTATED                                                                                              9
  AMP PEAK 13(11P13) WILD-TYPE                                                                                           68
D13V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 13(11P13) 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)                          9
                                                                                              clus
vv                                                                                             AMP PEAK 13(11P13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V30, binary
                              cls
clus                            0  1
  AMP PEAK 13(11P13) MUTATED    2  5
  AMP PEAK 13(11P13) WILD-TYPE 52 54
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      2    5
  AMP PEAK 13(11P13) WILD-TYPE   52   54
         clus
vv        AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  ABSENT                           2                           52
  PRESENT                          5                           54
[1] 2 2
[1] FALSE
D13V31, continuous
D13V32, continuous
D13V33, binary
                              cls
clus                            0  1
  AMP PEAK 13(11P13) MUTATED    1  7
  AMP PEAK 13(11P13) WILD-TYPE 34 74
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      1    7
  AMP PEAK 13(11P13) WILD-TYPE   34   74
                                          clus
vv                                         AMP PEAK 13(11P13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              1
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          7
                                          clus
vv                                         AMP PEAK 13(11P13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           74
[1] 2 2
[1] FALSE
D13V34, continuous
                              vv
clus                           OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 13(11P13) MUTATED       0                    6                   0
  AMP PEAK 13(11P13) WILD-TYPE     3                  107                   5
D13V35, multiclass
                      clus
vv                     AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  OTHER                                         0                            3
  RADICAL HYSTERECTOMY                          6                          107
  SIMPLE HYSTERECTOMY                           0                            5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 13(11P13) MUTATED              1           4          3
  AMP PEAK 13(11P13) WILD-TYPE            7          36         37
D13V36, multiclass
              clus
vv             AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  CURRENT USER                          1                            7
  FORMER USER                           4                           36
  NEVER USED                            3                           37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V37, continuous
D13V38, binary
                              cls
clus                            0  1
  AMP PEAK 13(11P13) MUTATED    6  1
  AMP PEAK 13(11P13) WILD-TYPE 67 13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      6    1
  AMP PEAK 13(11P13) WILD-TYPE   67   13
         clus
vv        AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  ABSENT                           6                           67
  PRESENT                          1                           13
[1] 2 2
[1] FALSE
D13V39, continuous
[1] "Remove cluster labels:"     "AMP PEAK 13(11P13) MUTATED"
clus
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                           1                            8 
                  TCGA-C5-A1MH                   TCGA-C5-A1MN 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-C5-A1MP                   TCGA-EK-A2RO 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-HM-A3JK                   TCGA-JW-A852 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-MU-A51Y                   TCGA-MU-A8JM 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK 13(11P13) MUTATED     0    0   1    1    1  0   0    2    0   3   1
  AMP PEAK 13(11P13) WILD-TYPE   2    1  21   50   20  3   6    4    8  10   1
                              vv
clus                           T4 TX
  AMP PEAK 13(11P13) MUTATED    0  1
  AMP PEAK 13(11P13) WILD-TYPE  1  6
D13V40, multiclass
      clus
vv     AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  T1A                           0                            2
  T1A1                          0                            1
  T1B                           1                           21
  T1B1                          1                           50
  T1B2                          1                           20
  T2                            0                            3
  T2A                           0                            6
  T2A1                          2                            4
  T2A2                          0                            8
  T2B                           3                           10
  T3B                           1                            1
  T4                            0                            1
  TX                            1                            6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V41, continuous

Clustering(14) Variable = AMP PEAK 14(11Q13.3) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(11Q13.3) MUTATED    15   6
  AMP PEAK 14(11Q13.3) WILD-TYPE 122  26
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            21                            148 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                             6                             26 
$`AMP PEAK 14(11Q13.3) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MF 
       11.44        68.84       144.16         5.46        35.01        53.16 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A7UC TCGA-DS-A7WI TCGA-EA-A1QT 
       73.18        73.45        25.35        17.19         8.28        12.36 
TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-FU-A40J TCGA-IR-A3LA TCGA-IR-A3LH TCGA-JW-A5VK 
        6.64         1.18         1.35       137.16        78.71        20.48 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-Q1-A6DT 
        0.07         0.82         3.39 

$`AMP PEAK 14(11Q13.3) 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-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       30.21        57.73        38.99        35.61         0.46         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       40.93         3.58        44.22        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43         0.82        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      182.93       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       85.55        60.69        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ 
       22.98        16.83        16.18         7.33         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         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG 
       14.96        13.58        13.48        12.59        45.96         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        0.59         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         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        1.45         1.58         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
        4.11       147.39        66.81       117.40        96.95        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       26.56        36.36        14.43        16.64        19.33        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A5YI 
       10.06         5.13         0.10         0.89        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        3.45         5.85         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                        144.16                         182.93 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                         17.19                          13.53 
[1] "0.1 - 144.2 (17.2)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.2"
D14V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK 14(11Q13.3) MUTATED   13        4
  AMP PEAK 14(11Q13.3) WILD-TYPE 84       35
D14V3, multiclass
          clus
vv         AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  T1                                 13                             84
  T2+T3+T4                            4                             35
[1] 2 2
[1] FALSE
D14V4, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q13.3) MUTATED   10  6
  AMP PEAK 14(11Q13.3) WILD-TYPE 77 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED     10    6
  AMP PEAK 14(11Q13.3) WILD-TYPE   77   34
   clus
vv  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  0                           10                             77
  1                            6                             34
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 14(11Q13.3) MUTATED    8  0 10
  AMP PEAK 14(11Q13.3) WILD-TYPE 64  3 55
D14V5, multiclass
    clus
vv   AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  M0                            8                             64
  M1                            0                              3
  MX                           10                             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(11Q13.3) MUTATED               0                               19
  AMP PEAK 14(11Q13.3) WILD-TYPE             2                              125
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 14(11Q13.3) MUTATED                                               0
  AMP PEAK 14(11Q13.3) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 14(11Q13.3) MUTATED                                     2
  AMP PEAK 14(11Q13.3) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 14(11Q13.3) MUTATED                                           1
  AMP PEAK 14(11Q13.3) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 14(11Q13.3) MUTATED                                              0
  AMP PEAK 14(11Q13.3) WILD-TYPE                                            4
D14V6, multiclass
                                               clus
vv                                              AMP PEAK 14(11Q13.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        19
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              AMP PEAK 14(11Q13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         125
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q13.3) MUTATED     7  15
  AMP PEAK 14(11Q13.3) WILD-TYPE  20 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      7   15
  AMP PEAK 14(11Q13.3) WILD-TYPE   20  134
     clus
vv    AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  NO                             7                             20
  YES                           15                            134
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(11Q13.3) MUTATED                                  0     2
  AMP PEAK 14(11Q13.3) WILD-TYPE                                7    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(11Q13.3) MUTATED                           4
  AMP PEAK 14(11Q13.3) WILD-TYPE                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 14(11Q13.3) MUTATED                                           0
  AMP PEAK 14(11Q13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 14(11Q13.3) MUTATED      16
  AMP PEAK 14(11Q13.3) WILD-TYPE   114
D14V10, multiclass
                                           clus
vv                                          AMP PEAK 14(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               16
                                           clus
vv                                          AMP PEAK 14(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q13.3) MUTATED     0  15
  AMP PEAK 14(11Q13.3) WILD-TYPE  11 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      0   15
  AMP PEAK 14(11Q13.3) WILD-TYPE   11  112
                        clus
vv                       AMP PEAK 14(11Q13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       AMP PEAK 14(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            112
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q13.3) MUTATED    7  5
  AMP PEAK 14(11Q13.3) WILD-TYPE 41 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      7    5
  AMP PEAK 14(11Q13.3) WILD-TYPE   41   14
            clus
vv           AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  TUMOR FREE                            7                             41
  WITH TUMOR                            5                             14
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 14(11Q13.3) MUTATED         0      1       0            19       2
  AMP PEAK 14(11Q13.3) WILD-TYPE       1      9       6           128      10
D14V14, multiclass
               clus
vv              AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   1                              9
  UKRAINE                                  0                              6
  UNITED STATES                           19                            128
  VIETNAM                                  2                             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 14(11Q13.3) MUTATED    0  7 13  1  1
  AMP PEAK 14(11Q13.3) WILD-TYPE 14 76 59  0  4
D14V15, multiclass
    clus
vv   AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  G1                            0                             14
  G2                            7                             76
  G3                           13                             59
  G4                            1                              0
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V16, continuous
D14V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 14(11Q13.3) MUTATED                                             3
  AMP PEAK 14(11Q13.3) WILD-TYPE                                          18
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 14(11Q13.3) MUTATED                                        2
  AMP PEAK 14(11Q13.3) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 14(11Q13.3) MUTATED                                                 0
  AMP PEAK 14(11Q13.3) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 14(11Q13.3) MUTATED                3                  10
  AMP PEAK 14(11Q13.3) WILD-TYPE             33                  73
D14V18, multiclass
                                                 clus
vv                                                AMP PEAK 14(11Q13.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             3
  LIFELONG NON-SMOKER                                                       10
                                                 clus
vv                                                AMP PEAK 14(11Q13.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              33
  LIFELONG NON-SMOKER                                                         73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 14(11Q13.3) MUTATED             4        3             3        0
  AMP PEAK 14(11Q13.3) WILD-TYPE          13       34             8        5
D14V20, multiclass
               clus
vv              AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  COMBINATION                              4                             13
  EXTERNAL                                 3                             34
  EXTERNAL BEAM                            3                              8
  INTERNAL                                 0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V21, binary
                                cls
clus                             0 1
  AMP PEAK 14(11Q13.3) MUTATED   2 0
  AMP PEAK 14(11Q13.3) WILD-TYPE 9 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      2    0
  AMP PEAK 14(11Q13.3) WILD-TYPE    9    3
     clus
vv    AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  CGY                            2                              9
  GY                             0                              3
[1] 2 2
[1] FALSE
D14V22, continuous
D14V23, continuous
D14V24, continuous
D14V25, continuous
D14V26, continuous
D14V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 14(11Q13.3) MUTATED                                     0
  AMP PEAK 14(11Q13.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 14(11Q13.3) MUTATED                                     1
  AMP PEAK 14(11Q13.3) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 14(11Q13.3) MUTATED                         1
  AMP PEAK 14(11Q13.3) WILD-TYPE                       8
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 14(11Q13.3) MUTATED                         0
  AMP PEAK 14(11Q13.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 14(11Q13.3) MUTATED                         1
  AMP PEAK 14(11Q13.3) WILD-TYPE                       4
D14V28, multiclass
                                     clus
vv                                    AMP PEAK 14(11Q13.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        1
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 14(11Q13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          8
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  AMP PEAK 14(11Q13.3) MUTATED                                               0
  AMP PEAK 14(11Q13.3) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 14(11Q13.3) MUTATED                                                1
  AMP PEAK 14(11Q13.3) WILD-TYPE                                              9
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 14(11Q13.3) MUTATED                                                                                   4
  AMP PEAK 14(11Q13.3) WILD-TYPE                                                                                50
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 14(11Q13.3) MUTATED                                                                                             12
  AMP PEAK 14(11Q13.3) WILD-TYPE                                                                                           65
D14V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 14(11Q13.3) 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                                                                                             AMP PEAK 14(11Q13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        50
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             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"
D14V30, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q13.3) MUTATED    6  8
  AMP PEAK 14(11Q13.3) WILD-TYPE 48 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      6    8
  AMP PEAK 14(11Q13.3) WILD-TYPE   48   51
         clus
vv        AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  ABSENT                             6                             48
  PRESENT                            8                             51
[1] 2 2
[1] FALSE
D14V31, continuous
D14V32, continuous
D14V33, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q13.3) MUTATED    4 10
  AMP PEAK 14(11Q13.3) WILD-TYPE 31 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      4   10
  AMP PEAK 14(11Q13.3) WILD-TYPE   31   71
                                          clus
vv                                         AMP PEAK 14(11Q13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           10
                                          clus
vv                                         AMP PEAK 14(11Q13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             71
[1] 2 2
[1] FALSE
D14V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 14(11Q13.3) MUTATED       0                   14                   2
  AMP PEAK 14(11Q13.3) WILD-TYPE     3                   99                   3
D14V35, multiclass
                      clus
vv                     AMP PEAK 14(11Q13.3) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           14
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     AMP PEAK 14(11Q13.3) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             99
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 14(11Q13.3) MUTATED              1           3          7
  AMP PEAK 14(11Q13.3) WILD-TYPE            7          37         33
D14V36, multiclass
              clus
vv             AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  CURRENT USER                            1                              7
  FORMER USER                             3                             37
  NEVER USED                              7                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V37, continuous
D14V38, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q13.3) MUTATED   10  1
  AMP PEAK 14(11Q13.3) WILD-TYPE 63 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED     10    1
  AMP PEAK 14(11Q13.3) WILD-TYPE   63   13
         clus
vv        AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  ABSENT                            10                             63
  PRESENT                            1                             13
[1] 2 2
[1] FALSE
D14V39, continuous
[1] "Remove cluster labels:"       "AMP PEAK 14(11Q13.3) MUTATED"
clus
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                             1                              8 
                    TCGA-C5-A1MH                     TCGA-C5-A1MN 
"AMP PEAK 14(11Q13.3) WILD-TYPE" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"AMP PEAK 14(11Q13.3) WILD-TYPE" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"AMP PEAK 14(11Q13.3) WILD-TYPE" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"AMP PEAK 14(11Q13.3) WILD-TYPE" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 14(11Q13.3) MUTATED     1    0   6    3    3  0   0    2    1   0
  AMP PEAK 14(11Q13.3) WILD-TYPE   1    1  16   48   18  3   6    4    7  13
                                vv
clus                             T3B T4 TX
  AMP PEAK 14(11Q13.3) MUTATED     1  0  1
  AMP PEAK 14(11Q13.3) WILD-TYPE   1  1  6
D14V40, multiclass
      clus
vv     AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             6                             16
  T1B1                            3                             48
  T1B2                            3                             18
  T2                              0                              3
  T2A                             0                              6
  T2A1                            2                              4
  T2A2                            1                              7
  T2B                             0                             13
  T3B                             1                              1
  T4                              0                              1
  TX                              1                              6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V41, continuous

Clustering(15) Variable = AMP PEAK 15(11Q22.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(11Q22.1) MUTATED    22   9
  AMP PEAK 15(11Q22.1) WILD-TYPE 115  23
  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE 
                            31                            138 
  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE 
                             9                             23 
$`AMP PEAK 15(11Q22.1) MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M9 
       23.67        11.44       144.16       177.04         5.46        35.01 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7X5 
       73.18        73.45        78.35        25.35        17.19        13.61 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A3QE 
       87.75        36.76         2.66         8.28        13.05         1.18 
TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.81        13.91         6.64         1.18         0.07         0.10 
TCGA-EX-A3L1 TCGA-FU-A40J TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-LP-A4AX TCGA-RA-A741 
        6.94         1.35        21.67        78.71         0.07         3.88 
TCGA-UC-A7PD 
       11.67 

$`AMP PEAK 15(11Q22.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BL 
       49.48        57.04        68.84        18.74        36.56       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
       82.85        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       57.73        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
       40.93         3.58        44.22        83.05       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        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-A7UE 
      101.82       134.33        15.48         9.67        73.41        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VM 
       60.69        94.95         9.34         2.73        58.88       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
      118.65        22.98        16.83        16.18         7.33         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 
       12.36         1.74         1.32         0.82         0.62        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35        14.50        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       14.89         1.48         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       13.48        12.59        45.96         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        4.04         0.03         0.36        23.70         2.24         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.03        20.35         7.92        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF 
        3.72         5.75         4.80         6.25        19.59        93.99 

  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE 
                        177.04                         182.93 
  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE 
                        13.050                         13.725 
[1] "0.1 - 177.0 (13.1)" "0.0 - 182.9 (13.7)"
[1] "hr=" "1.6"
D15V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK 15(11Q22.1) MUTATED   20        5
  AMP PEAK 15(11Q22.1) WILD-TYPE 77       34
D15V3, multiclass
          clus
vv         AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  T1                                 20                             77
  T2+T3+T4                            5                             34
[1] 2 2
[1] FALSE
D15V4, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q22.1) MUTATED   17  8
  AMP PEAK 15(11Q22.1) WILD-TYPE 70 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q22.1) MUTATED     17    8
  AMP PEAK 15(11Q22.1) WILD-TYPE   70   32
   clus
vv  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  0                           17                             70
  1                            8                             32
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 15(11Q22.1) MUTATED   16  0  8
  AMP PEAK 15(11Q22.1) WILD-TYPE 56  3 57
D15V5, multiclass
    clus
vv   AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  M0                           16                             56
  M1                            0                              3
  MX                            8                             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(11Q22.1) MUTATED               0                               29
  AMP PEAK 15(11Q22.1) WILD-TYPE             2                              115
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 15(11Q22.1) MUTATED                                               0
  AMP PEAK 15(11Q22.1) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 15(11Q22.1) MUTATED                                     2
  AMP PEAK 15(11Q22.1) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 15(11Q22.1) MUTATED                                           0
  AMP PEAK 15(11Q22.1) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 15(11Q22.1) MUTATED                                              0
  AMP PEAK 15(11Q22.1) WILD-TYPE                                            4
D15V6, multiclass
                                               clus
vv                                              AMP PEAK 15(11Q22.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        29
  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                                              AMP PEAK 15(11Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         115
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q22.1) MUTATED     7  24
  AMP PEAK 15(11Q22.1) WILD-TYPE  20 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q22.1) MUTATED      7   24
  AMP PEAK 15(11Q22.1) WILD-TYPE   20  125
     clus
vv    AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  NO                             7                             20
  YES                           24                            125
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(11Q22.1) MUTATED                                  2     2
  AMP PEAK 15(11Q22.1) WILD-TYPE                                5    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(11Q22.1) MUTATED                           6
  AMP PEAK 15(11Q22.1) WILD-TYPE                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 15(11Q22.1) MUTATED                                           1
  AMP PEAK 15(11Q22.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 15(11Q22.1) MUTATED      20
  AMP PEAK 15(11Q22.1) WILD-TYPE   110
D15V10, multiclass
                                           clus
vv                                          AMP PEAK 15(11Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               20
                                           clus
vv                                          AMP PEAK 15(11Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D15V11, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q22.1) MUTATED     1  23
  AMP PEAK 15(11Q22.1) WILD-TYPE  10 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q22.1) MUTATED      1   23
  AMP PEAK 15(11Q22.1) WILD-TYPE   10  104
                        clus
vv                       AMP PEAK 15(11Q22.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       AMP PEAK 15(11Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            104
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q22.1) MUTATED   10  5
  AMP PEAK 15(11Q22.1) WILD-TYPE 38 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q22.1) MUTATED     10    5
  AMP PEAK 15(11Q22.1) WILD-TYPE   38   14
            clus
vv           AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  TUMOR FREE                           10                             38
  WITH TUMOR                            5                             14
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 15(11Q22.1) MUTATED         0      1       2            27       1
  AMP PEAK 15(11Q22.1) WILD-TYPE       1      9       4           120      11
D15V14, multiclass
               clus
vv              AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   1                              9
  UKRAINE                                  2                              4
  UNITED STATES                           27                            120
  VIETNAM                                  1                             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 15(11Q22.1) MUTATED    1 10 18  1  1
  AMP PEAK 15(11Q22.1) WILD-TYPE 13 73 54  0  4
D15V15, multiclass
    clus
vv   AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  G1                            1                             13
  G2                           10                             73
  G3                           18                             54
  G4                            1                              0
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V16, continuous
D15V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 15(11Q22.1) MUTATED                                             4
  AMP PEAK 15(11Q22.1) WILD-TYPE                                          17
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 15(11Q22.1) MUTATED                                        0
  AMP PEAK 15(11Q22.1) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 15(11Q22.1) MUTATED                                                 0
  AMP PEAK 15(11Q22.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 15(11Q22.1) MUTATED                4                  15
  AMP PEAK 15(11Q22.1) WILD-TYPE             32                  68
D15V18, multiclass
                                                 clus
vv                                                AMP PEAK 15(11Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             4
  LIFELONG NON-SMOKER                                                       15
                                                 clus
vv                                                AMP PEAK 15(11Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              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"
D15V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 15(11Q22.1) MUTATED             3        6             5        2
  AMP PEAK 15(11Q22.1) WILD-TYPE          14       31             6        3
D15V20, multiclass
               clus
vv              AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  COMBINATION                              3                             14
  EXTERNAL                                 6                             31
  EXTERNAL BEAM                            5                              6
  INTERNAL                                 2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V21, binary
                                cls
clus                             0 1
  AMP PEAK 15(11Q22.1) MUTATED   4 1
  AMP PEAK 15(11Q22.1) WILD-TYPE 7 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q22.1) MUTATED      4    1
  AMP PEAK 15(11Q22.1) WILD-TYPE    7    2
     clus
vv    AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  CGY                            4                              7
  GY                             1                              2
[1] 2 2
[1] FALSE
D15V22, continuous
D15V23, continuous
D15V24, continuous
D15V25, continuous
D15V26, continuous
D15V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 15(11Q22.1) MUTATED                                     1
  AMP PEAK 15(11Q22.1) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 15(11Q22.1) MUTATED                                     2
  AMP PEAK 15(11Q22.1) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 15(11Q22.1) MUTATED                         2
  AMP PEAK 15(11Q22.1) WILD-TYPE                       7
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 15(11Q22.1) MUTATED                         0
  AMP PEAK 15(11Q22.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 15(11Q22.1) MUTATED                         2
  AMP PEAK 15(11Q22.1) WILD-TYPE                       3
D15V28, multiclass
                                     clus
vv                                    AMP PEAK 15(11Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        2
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    AMP PEAK 15(11Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                          7
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  AMP PEAK 15(11Q22.1) MUTATED                                               0
  AMP PEAK 15(11Q22.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 15(11Q22.1) MUTATED                                                1
  AMP PEAK 15(11Q22.1) WILD-TYPE                                              9
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 15(11Q22.1) MUTATED                                                                                   3
  AMP PEAK 15(11Q22.1) WILD-TYPE                                                                                51
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 15(11Q22.1) MUTATED                                                                                             20
  AMP PEAK 15(11Q22.1) WILD-TYPE                                                                                           57
D15V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 15(11Q22.1) 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)                           20
                                                                                              clus
vv                                                                                             AMP PEAK 15(11Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V30, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q22.1) MUTATED   10 12
  AMP PEAK 15(11Q22.1) WILD-TYPE 44 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q22.1) MUTATED     10   12
  AMP PEAK 15(11Q22.1) WILD-TYPE   44   47
         clus
vv        AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  ABSENT                            10                             44
  PRESENT                           12                             47
[1] 2 2
[1] FALSE
D15V31, continuous
D15V32, continuous
D15V33, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q22.1) MUTATED   10 15
  AMP PEAK 15(11Q22.1) WILD-TYPE 25 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q22.1) MUTATED     10   15
  AMP PEAK 15(11Q22.1) WILD-TYPE   25   66
                                          clus
vv                                         AMP PEAK 15(11Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           15
                                          clus
vv                                         AMP PEAK 15(11Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             66
[1] 2 2
[1] FALSE
D15V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 15(11Q22.1) MUTATED       0                   22                   1
  AMP PEAK 15(11Q22.1) WILD-TYPE     3                   91                   4
D15V35, multiclass
                      clus
vv                     AMP PEAK 15(11Q22.1) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           22
  SIMPLE HYSTERECTOMY                             1
                      clus
vv                     AMP PEAK 15(11Q22.1) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             91
  SIMPLE HYSTERECTOMY                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 15(11Q22.1) MUTATED              2           6          9
  AMP PEAK 15(11Q22.1) WILD-TYPE            6          34         31
D15V36, multiclass
              clus
vv             AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                             6                             34
  NEVER USED                              9                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V37, continuous
D15V38, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q22.1) MUTATED   15  1
  AMP PEAK 15(11Q22.1) WILD-TYPE 58 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q22.1) MUTATED     15    1
  AMP PEAK 15(11Q22.1) WILD-TYPE   58   13
         clus
vv        AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  ABSENT                            15                             58
  PRESENT                            1                             13
[1] 2 2
[1] FALSE
D15V39, continuous
[1] "Remove cluster labels:"       "AMP PEAK 15(11Q22.1) MUTATED"
clus
  AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1MH                     TCGA-C5-A1MN 
"AMP PEAK 15(11Q22.1) WILD-TYPE" "AMP PEAK 15(11Q22.1) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-HM-A3JK 
"AMP PEAK 15(11Q22.1) WILD-TYPE" "AMP PEAK 15(11Q22.1) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-MU-A51Y 
"AMP PEAK 15(11Q22.1) WILD-TYPE" "AMP PEAK 15(11Q22.1) WILD-TYPE" 
                    TCGA-MU-A8JM 
"AMP PEAK 15(11Q22.1) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 15(11Q22.1) MUTATED     0    0   7   11    2  0   0    3    1   0
  AMP PEAK 15(11Q22.1) WILD-TYPE   2    1  15   40   19  3   6    3    7  13
                                vv
clus                             T3B T4 TX
  AMP PEAK 15(11Q22.1) MUTATED     1  0  0
  AMP PEAK 15(11Q22.1) WILD-TYPE   1  1  7
D15V40, multiclass
      clus
vv     AMP PEAK 15(11Q22.1) MUTATED AMP PEAK 15(11Q22.1) WILD-TYPE
  T1A                             0                              2
  T1A1                            0                              1
  T1B                             7                             15
  T1B1                           11                             40
  T1B2                            2                             19
  T2                              0                              3
  T2A                             0                              6
  T2A1                            3                              3
  T2A2                            1                              7
  T2B                             0                             13
  T3B                             1                              1
  T4                              0                              1
  TX                              0                              7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V41, continuous

Clustering(16) Variable = AMP PEAK 16(13Q22.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(13Q22.1) MUTATED    29  10
  AMP PEAK 16(13Q22.1) WILD-TYPE 108  22
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                            39                            130 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                            10                             22 
$`AMP PEAK 16(13Q22.1) MUTATED`
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LZ 
       82.85         5.46        35.01         0.46         3.58       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7X5 
       38.43        52.01        17.85       182.93        25.35        13.61 
TCGA-C5-A7X8 TCGA-DS-A0VM TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A44S TCGA-EA-A50E 
        2.73       117.99         0.62        13.05        12.66         0.26 
TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RE TCGA-EK-A2RJ 
       13.91        14.96        45.96         0.53         0.36         1.18 
TCGA-EK-A2RM TCGA-EK-A3GN TCGA-FU-A3HY TCGA-FU-A40J TCGA-FU-A5XV TCGA-IR-A3L7 
        2.24         0.03         0.66         1.35         1.97       147.39 
TCGA-IR-A3LB TCGA-IR-A3LK TCGA-JW-A5VJ TCGA-LP-A4AW TCGA-MY-A5BE TCGA-PN-A8MA 
       66.81        26.56        19.33         0.89         0.07         2.96 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73R 
        3.45         3.39         6.25 

$`AMP PEAK 16(13Q22.1) 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-A1BQ TCGA-C5-A1M5 
       36.56       144.16       177.04       173.29        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       31.40        46.32        30.21        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       35.61         2.43        40.93        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CJ 
       83.05        78.35         0.82        18.02        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       60.69        94.95         9.34        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-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-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       12.82        14.89         1.48         0.69        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       13.48        12.59         6.64         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.03        23.70         0.10         0.07         0.10         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84         0.92         2.17         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 
        1.58         1.48         0.82         3.52         1.32         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA 
       25.41        21.67        20.78        14.93         4.11       137.16 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU 
       16.64        20.48        15.58        10.06         5.13         0.10 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        4.34         3.72         5.85         3.72         5.75         4.80 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                        182.93                         177.04 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                         6.250                         14.465 
[1] "0.0 - 182.9 (6.2)"  "0.0 - 177.0 (14.5)"
[1] "hr=" "1.6"
D16V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK 16(13Q22.1) MUTATED   17        9
  AMP PEAK 16(13Q22.1) WILD-TYPE 80       30
D16V3, multiclass
          clus
vv         AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  T1                                 17                             80
  T2+T3+T4                            9                             30
[1] 2 2
[1] FALSE
D16V4, binary
                                cls
clus                              0  1
  AMP PEAK 16(13Q22.1) MUTATED   13 11
  AMP PEAK 16(13Q22.1) WILD-TYPE 74 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED     13   11
  AMP PEAK 16(13Q22.1) WILD-TYPE   74   29
   clus
vv  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  0                           13                             74
  1                           11                             29
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 16(13Q22.1) MUTATED   14  0 15
  AMP PEAK 16(13Q22.1) WILD-TYPE 58  3 50
D16V5, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  M0                           14                             58
  M1                            0                              3
  MX                           15                             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED               0                               31
  AMP PEAK 16(13Q22.1) WILD-TYPE             2                              113
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 16(13Q22.1) MUTATED                                               0
  AMP PEAK 16(13Q22.1) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                                     6
  AMP PEAK 16(13Q22.1) WILD-TYPE                                  14
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 16(13Q22.1) MUTATED                                           0
  AMP PEAK 16(13Q22.1) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 16(13Q22.1) MUTATED                                              2
  AMP PEAK 16(13Q22.1) WILD-TYPE                                            2
D16V6, multiclass
                                               clus
vv                                              AMP PEAK 16(13Q22.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        31
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              AMP PEAK 16(13Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         113
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       14
  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"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED     4  35
  AMP PEAK 16(13Q22.1) WILD-TYPE  23 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      4   35
  AMP PEAK 16(13Q22.1) WILD-TYPE   23  114
     clus
vv    AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  NO                             4                             23
  YES                           35                            114
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(13Q22.1) MUTATED                                  1     3
  AMP PEAK 16(13Q22.1) WILD-TYPE                                6    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(13Q22.1) MUTATED                           6
  AMP PEAK 16(13Q22.1) WILD-TYPE                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 16(13Q22.1) MUTATED                                           0
  AMP PEAK 16(13Q22.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 16(13Q22.1) MUTATED      29
  AMP PEAK 16(13Q22.1) WILD-TYPE   101
D16V10, multiclass
                                           clus
vv                                          AMP PEAK 16(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               29
                                           clus
vv                                          AMP PEAK 16(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D16V11, binary
                                cls
clus                              0  1
  AMP PEAK 16(13Q22.1) MUTATED    1 31
  AMP PEAK 16(13Q22.1) WILD-TYPE 10 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      1   31
  AMP PEAK 16(13Q22.1) WILD-TYPE   10   96
                        clus
vv                       AMP PEAK 16(13Q22.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       AMP PEAK 16(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             96
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                                cls
clus                              0  1
  AMP PEAK 16(13Q22.1) MUTATED    9  8
  AMP PEAK 16(13Q22.1) WILD-TYPE 39 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      9    8
  AMP PEAK 16(13Q22.1) WILD-TYPE   39   11
            clus
vv           AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  TUMOR FREE                            9                             39
  WITH TUMOR                            8                             11
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 16(13Q22.1) MUTATED         1      1       2            32       3
  AMP PEAK 16(13Q22.1) WILD-TYPE       0      9       4           115       9
D16V14, multiclass
               clus
vv              AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  NIGERIA                                  1                              0
  RUSSIA                                   1                              9
  UKRAINE                                  2                              4
  UNITED STATES                           32                            115
  VIETNAM                                  3                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 16(13Q22.1) MUTATED    2 15 20  0  2
  AMP PEAK 16(13Q22.1) WILD-TYPE 12 68 52  1  3
D16V15, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  G1                            2                             12
  G2                           15                             68
  G3                           20                             52
  G4                            0                              1
  GX                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V16, continuous
D16V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 16(13Q22.1) MUTATED                                             3
  AMP PEAK 16(13Q22.1) WILD-TYPE                                          18
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 16(13Q22.1) MUTATED                                        1
  AMP PEAK 16(13Q22.1) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 16(13Q22.1) MUTATED                                                 0
  AMP PEAK 16(13Q22.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 16(13Q22.1) MUTATED                6                  21
  AMP PEAK 16(13Q22.1) WILD-TYPE             30                  62
D16V18, multiclass
                                                 clus
vv                                                AMP PEAK 16(13Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             6
  LIFELONG NON-SMOKER                                                       21
                                                 clus
vv                                                AMP PEAK 16(13Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              30
  LIFELONG NON-SMOKER                                                         62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 16(13Q22.1) MUTATED             3       11             1        0
  AMP PEAK 16(13Q22.1) WILD-TYPE          14       26            10        5
D16V20, multiclass
               clus
vv              AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  COMBINATION                              3                             14
  EXTERNAL                                11                             26
  EXTERNAL BEAM                            1                             10
  INTERNAL                                 0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V21, binary
                                cls
clus                              0  1
  AMP PEAK 16(13Q22.1) MUTATED    0  0
  AMP PEAK 16(13Q22.1) WILD-TYPE 11  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      0    0
  AMP PEAK 16(13Q22.1) WILD-TYPE   11    3
D16V22, continuous
D16V23, continuous
D16V24, continuous
D16V25, continuous
D16V26, continuous
D16V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 16(13Q22.1) MUTATED                                     0
  AMP PEAK 16(13Q22.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 16(13Q22.1) MUTATED                                     1
  AMP PEAK 16(13Q22.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 16(13Q22.1) MUTATED                         1
  AMP PEAK 16(13Q22.1) WILD-TYPE                       8
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 16(13Q22.1) MUTATED                         1
  AMP PEAK 16(13Q22.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 16(13Q22.1) MUTATED                         1
  AMP PEAK 16(13Q22.1) WILD-TYPE                       4
D16V28, multiclass
                                     clus
vv                                    AMP PEAK 16(13Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        1
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 16(13Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          8
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          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)
  AMP PEAK 16(13Q22.1) MUTATED                                               0
  AMP PEAK 16(13Q22.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 16(13Q22.1) MUTATED                                                2
  AMP PEAK 16(13Q22.1) WILD-TYPE                                              8
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 16(13Q22.1) MUTATED                                                                                  13
  AMP PEAK 16(13Q22.1) WILD-TYPE                                                                                41
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 16(13Q22.1) MUTATED                                                                                             16
  AMP PEAK 16(13Q22.1) WILD-TYPE                                                                                           61
D16V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 16(13Q22.1) 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)                           16
                                                                                              clus
vv                                                                                             AMP PEAK 16(13Q22.1) 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)                                        41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V30, binary
                                cls
clus                              0  1
  AMP PEAK 16(13Q22.1) MUTATED    7 17
  AMP PEAK 16(13Q22.1) WILD-TYPE 47 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      7   17
  AMP PEAK 16(13Q22.1) WILD-TYPE   47   42
         clus
vv        AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  ABSENT                             7                             47
  PRESENT                           17                             42
[1] 2 2
[1] FALSE
D16V31, continuous
D16V32, continuous
D16V33, binary
                                cls
clus                              0  1
  AMP PEAK 16(13Q22.1) MUTATED    7 16
  AMP PEAK 16(13Q22.1) WILD-TYPE 28 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      7   16
  AMP PEAK 16(13Q22.1) WILD-TYPE   28   65
                                          clus
vv                                         AMP PEAK 16(13Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           16
                                          clus
vv                                         AMP PEAK 16(13Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             65
[1] 2 2
[1] FALSE
D16V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 16(13Q22.1) MUTATED       1                   22                   0
  AMP PEAK 16(13Q22.1) WILD-TYPE     2                   91                   5
D16V35, multiclass
                      clus
vv                     AMP PEAK 16(13Q22.1) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           22
  SIMPLE HYSTERECTOMY                             0
                      clus
vv                     AMP PEAK 16(13Q22.1) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             91
  SIMPLE HYSTERECTOMY                               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 16(13Q22.1) MUTATED              0          11          8
  AMP PEAK 16(13Q22.1) WILD-TYPE            8          29         32
D16V36, multiclass
              clus
vv             AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  CURRENT USER                            0                              8
  FORMER USER                            11                             29
  NEVER USED                              8                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V37, continuous
D16V38, binary
                                cls
clus                              0  1
  AMP PEAK 16(13Q22.1) MUTATED   14  2
  AMP PEAK 16(13Q22.1) WILD-TYPE 59 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED     14    2
  AMP PEAK 16(13Q22.1) WILD-TYPE   59   12
         clus
vv        AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  ABSENT                            14                             59
  PRESENT                            2                             12
[1] 2 2
[1] FALSE
D16V39, continuous
[1] "Remove cluster labels:"       "AMP PEAK 16(13Q22.1) MUTATED"
clus
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1MH                     TCGA-C5-A1MN 
"AMP PEAK 16(13Q22.1) WILD-TYPE" "AMP PEAK 16(13Q22.1) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-HM-A3JK 
"AMP PEAK 16(13Q22.1) WILD-TYPE" "AMP PEAK 16(13Q22.1) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-MU-A51Y 
"AMP PEAK 16(13Q22.1) WILD-TYPE" "AMP PEAK 16(13Q22.1) WILD-TYPE" 
                    TCGA-MU-A8JM 
"AMP PEAK 16(13Q22.1) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 16(13Q22.1) MUTATED     1    0   2    8    6  1   1    1    2   2
  AMP PEAK 16(13Q22.1) WILD-TYPE   1    1  20   43   15  2   5    5    6  11
                                vv
clus                             T3B T4 TX
  AMP PEAK 16(13Q22.1) MUTATED     1  1  4
  AMP PEAK 16(13Q22.1) WILD-TYPE   1  0  3
D16V40, multiclass
      clus
vv     AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             2                             20
  T1B1                            8                             43
  T1B2                            6                             15
  T2                              1                              2
  T2A                             1                              5
  T2A1                            1                              5
  T2A2                            2                              6
  T2B                             2                             11
  T3B                             1                              1
  T4                              1                              0
  TX                              4                              3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V41, continuous

Clustering(17) Variable = AMP PEAK 17(15Q26.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(15Q26.1) MUTATED    31  10
  AMP PEAK 17(15Q26.1) WILD-TYPE 106  22
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            41                            128 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            10                             22 
$`AMP PEAK 17(15Q26.1) MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1ME 
       49.48        18.74       177.04        31.40        30.21        57.73 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A2M2 
       35.61         2.43         3.58        73.18       100.14         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UI TCGA-C5-A7X3 
       52.01        18.02       101.82         9.67        94.95         9.34 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A50E 
        2.73        87.75         2.66         8.28         1.74         0.26 
TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EX-A3L1 
       14.89        13.91         4.04         0.03         2.24         6.94 
TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A5XV TCGA-HM-A3JK TCGA-IR-A3LA TCGA-JW-A5VG 
        4.47        23.84         1.97        20.78       137.16        14.43 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-LP-A4AU TCGA-MY-A5BE TCGA-R2-A69V 
       19.33        15.58         0.10         0.07        19.59 

$`AMP PEAK 17(15Q26.1) 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-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      173.29        82.85         5.46        19.86        67.46        46.32 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A2LS 
       35.01        53.16        38.99         0.46        40.93        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A3HF TCGA-C5-A3HL 
       73.45        83.05        78.35        38.43        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC 
      182.93        25.35       134.33        15.48        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       85.55        60.69        13.61        58.88        36.76       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
      118.65        22.98        16.83        16.18         7.33         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-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.82         1.48         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        0.07         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-A449 
        0.10         0.10         0.03        20.35         7.92        14.70 
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-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.32         1.12        25.41        21.67        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      147.39        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 
       26.56        36.36        16.64        20.48        10.06         5.13 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       29.72         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 
        3.39         3.72         5.75         4.80         6.25         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                        177.04                         182.93 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                        14.890                         12.935 
[1] "0.0 - 177.0 (14.9)" "0.0 - 182.9 (12.9)"
[1] "hr=" "1.3"
D17V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK 17(15Q26.1) MUTATED   19       12
  AMP PEAK 17(15Q26.1) WILD-TYPE 78       27
D17V3, multiclass
          clus
vv         AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  T1                                 19                             78
  T2+T3+T4                           12                             27
[1] 2 2
[1] FALSE
D17V4, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   19 10
  AMP PEAK 17(15Q26.1) WILD-TYPE 68 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     19   10
  AMP PEAK 17(15Q26.1) WILD-TYPE   68   30
   clus
vv  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  0                           19                             68
  1                           10                             30
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 17(15Q26.1) MUTATED   17  0 15
  AMP PEAK 17(15Q26.1) WILD-TYPE 55  3 50
D17V5, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  M0                           17                             55
  M1                            0                              3
  MX                           15                             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED               0                               36
  AMP PEAK 17(15Q26.1) WILD-TYPE             2                              108
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 17(15Q26.1) MUTATED                                               1
  AMP PEAK 17(15Q26.1) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                                     3
  AMP PEAK 17(15Q26.1) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 17(15Q26.1) MUTATED                                           2
  AMP PEAK 17(15Q26.1) WILD-TYPE                                         0
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 17(15Q26.1) MUTATED                                              1
  AMP PEAK 17(15Q26.1) WILD-TYPE                                            3
D17V6, multiclass
                                               clus
vv                                              AMP PEAK 17(15Q26.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        36
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              AMP PEAK 17(15Q26.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         108
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED     7  36
  AMP PEAK 17(15Q26.1) WILD-TYPE  20 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      7   36
  AMP PEAK 17(15Q26.1) WILD-TYPE   20  113
     clus
vv    AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  NO                             7                             20
  YES                           36                            113
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(15Q26.1) MUTATED                                  4     4
  AMP PEAK 17(15Q26.1) WILD-TYPE                                3    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(15Q26.1) MUTATED                           4
  AMP PEAK 17(15Q26.1) WILD-TYPE                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 17(15Q26.1) MUTATED                                           0
  AMP PEAK 17(15Q26.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 17(15Q26.1) MUTATED      30
  AMP PEAK 17(15Q26.1) WILD-TYPE   100
D17V10, multiclass
                                           clus
vv                                          AMP PEAK 17(15Q26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               30
                                           clus
vv                                          AMP PEAK 17(15Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D17V11, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED    5 31
  AMP PEAK 17(15Q26.1) WILD-TYPE  6 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      5   31
  AMP PEAK 17(15Q26.1) WILD-TYPE    6   96
                        clus
vv                       AMP PEAK 17(15Q26.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       AMP PEAK 17(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             96
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   13  8
  AMP PEAK 17(15Q26.1) WILD-TYPE 35 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     13    8
  AMP PEAK 17(15Q26.1) WILD-TYPE   35   11
            clus
vv           AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  TUMOR FREE                           13                             35
  WITH TUMOR                            8                             11
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 17(15Q26.1) MUTATED         0      2       1            38       2
  AMP PEAK 17(15Q26.1) WILD-TYPE       1      8       5           109      10
D17V14, multiclass
               clus
vv              AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  1                              5
  UNITED STATES                           38                            109
  VIETNAM                                  2                             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 17(15Q26.1) MUTATED    3 18 22  0  0
  AMP PEAK 17(15Q26.1) WILD-TYPE 11 65 50  1  5
D17V15, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  G1                            3                             11
  G2                           18                             65
  G3                           22                             50
  G4                            0                              1
  GX                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V16, continuous
D17V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 17(15Q26.1) MUTATED                                             6
  AMP PEAK 17(15Q26.1) WILD-TYPE                                          15
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 17(15Q26.1) MUTATED                                        0
  AMP PEAK 17(15Q26.1) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 17(15Q26.1) MUTATED                                                 0
  AMP PEAK 17(15Q26.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 17(15Q26.1) MUTATED                9                  24
  AMP PEAK 17(15Q26.1) WILD-TYPE             27                  59
D17V18, multiclass
                                                 clus
vv                                                AMP PEAK 17(15Q26.1) 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                                                             9
  LIFELONG NON-SMOKER                                                       24
                                                 clus
vv                                                AMP PEAK 17(15Q26.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              27
  LIFELONG NON-SMOKER                                                         59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 17(15Q26.1) MUTATED             4       12             3        0
  AMP PEAK 17(15Q26.1) WILD-TYPE          13       25             8        5
D17V20, multiclass
               clus
vv              AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  COMBINATION                              4                             13
  EXTERNAL                                12                             25
  EXTERNAL BEAM                            3                              8
  INTERNAL                                 0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V21, binary
                                cls
clus                             0 1
  AMP PEAK 17(15Q26.1) MUTATED   4 1
  AMP PEAK 17(15Q26.1) WILD-TYPE 7 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      4    1
  AMP PEAK 17(15Q26.1) WILD-TYPE    7    2
     clus
vv    AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  CGY                            4                              7
  GY                             1                              2
[1] 2 2
[1] FALSE
D17V22, continuous
D17V23, continuous
D17V24, continuous
D17V25, continuous
D17V26, continuous
D17V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 17(15Q26.1) MUTATED                                     0
  AMP PEAK 17(15Q26.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 17(15Q26.1) MUTATED                                     0
  AMP PEAK 17(15Q26.1) WILD-TYPE                                   6
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 17(15Q26.1) MUTATED                         1
  AMP PEAK 17(15Q26.1) WILD-TYPE                       8
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 17(15Q26.1) MUTATED                         1
  AMP PEAK 17(15Q26.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 17(15Q26.1) MUTATED                         0
  AMP PEAK 17(15Q26.1) WILD-TYPE                       5
D17V28, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 17(15Q26.1) MUTATED"
clus
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                             2                             21 
                    TCGA-BI-A20A                     TCGA-C5-A0TN 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-C5-A1BE                     TCGA-C5-A1BM 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-C5-A2LX                     TCGA-DR-A0ZM 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VM 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-DS-A0VN                     TCGA-DS-A3LQ 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-EK-A2RN                     TCGA-EK-A2RO 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-EX-A449 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-FU-A3EO                     TCGA-HM-A4S6 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-IR-A3LH                     TCGA-IR-A3LI 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-IR-A3LK                     TCGA-MU-A8JM 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-UC-A7PD 
"AMP PEAK 17(15Q26.1) WILD-TYPE" 
                                vv
clus                             INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  AMP PEAK 17(15Q26.1) MUTATED                                               1
  AMP PEAK 17(15Q26.1) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 17(15Q26.1) MUTATED                                                2
  AMP PEAK 17(15Q26.1) WILD-TYPE                                              8
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 17(15Q26.1) MUTATED                                                                                  14
  AMP PEAK 17(15Q26.1) WILD-TYPE                                                                                40
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 17(15Q26.1) MUTATED                                                                                             15
  AMP PEAK 17(15Q26.1) WILD-TYPE                                                                                           62
D17V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 17(15Q26.1) 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)                                      14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           15
                                                                                              clus
vv                                                                                             AMP PEAK 17(15Q26.1) 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)                                        40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V30, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   12 13
  AMP PEAK 17(15Q26.1) WILD-TYPE 42 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     12   13
  AMP PEAK 17(15Q26.1) WILD-TYPE   42   46
         clus
vv        AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  ABSENT                            12                             42
  PRESENT                           13                             46
[1] 2 2
[1] FALSE
D17V31, continuous
D17V32, continuous
D17V33, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED    6 18
  AMP PEAK 17(15Q26.1) WILD-TYPE 29 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      6   18
  AMP PEAK 17(15Q26.1) WILD-TYPE   29   63
                                          clus
vv                                         AMP PEAK 17(15Q26.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           18
                                          clus
vv                                         AMP PEAK 17(15Q26.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             63
[1] 2 2
[1] FALSE
D17V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 17(15Q26.1) MUTATED       0                   25                   2
  AMP PEAK 17(15Q26.1) WILD-TYPE     3                   88                   3
D17V35, multiclass
                      clus
vv                     AMP PEAK 17(15Q26.1) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           25
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     AMP PEAK 17(15Q26.1) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             88
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 17(15Q26.1) MUTATED              2           5         13
  AMP PEAK 17(15Q26.1) WILD-TYPE            6          35         27
D17V36, multiclass
              clus
vv             AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                             5                             35
  NEVER USED                             13                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V37, continuous
D17V38, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.1) MUTATED   14  3
  AMP PEAK 17(15Q26.1) WILD-TYPE 59 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     14    3
  AMP PEAK 17(15Q26.1) WILD-TYPE   59   11
         clus
vv        AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  ABSENT                            14                             59
  PRESENT                            3                             11
[1] 2 2
[1] FALSE
D17V39, continuous
[1] "Remove cluster labels:"       "AMP PEAK 17(15Q26.1) MUTATED"
clus
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-EK-A2RO 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-MU-A51Y 
"AMP PEAK 17(15Q26.1) WILD-TYPE" "AMP PEAK 17(15Q26.1) WILD-TYPE" 
                    TCGA-MU-A8JM 
"AMP PEAK 17(15Q26.1) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 17(15Q26.1) MUTATED     0    0   4   10    5  1   4    2    1   3
  AMP PEAK 17(15Q26.1) WILD-TYPE   2    1  18   41   16  2   2    4    7  10
                                vv
clus                             T3B T4 TX
  AMP PEAK 17(15Q26.1) MUTATED     0  1  1
  AMP PEAK 17(15Q26.1) WILD-TYPE   2  0  6
D17V40, multiclass
      clus
vv     AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  T1A                             0                              2
  T1A1                            0                              1
  T1B                             4                             18
  T1B1                           10                             41
  T1B2                            5                             16
  T2                              1                              2
  T2A                             4                              2
  T2A1                            2                              4
  T2A2                            1                              7
  T2B                             3                             10
  T3B                             0                              2
  T4                              1                              0
  TX                              1                              6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V41, continuous

Clustering(18) Variable = AMP PEAK 18(16P13.13) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 18(16P13.13) MUTATED    28   6
  AMP PEAK 18(16P13.13) WILD-TYPE 109  26
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                             34                             135 
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                              6                              26 
$`AMP PEAK 18(16P13.13) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       57.04        31.40        46.32        38.99        35.61         0.46 
TCGA-C5-A2LS TCGA-C5-A3HF TCGA-C5-A7CH TCGA-C5-A7X8 TCGA-DS-A3LQ TCGA-DS-A7WI 
       44.22        17.85        25.35         2.73        22.98         8.28 
TCGA-EA-A3HQ TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2RC 
        1.74        13.05        14.50        13.91        14.96         4.04 
TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-FU-A23L TCGA-FU-A3EO 
        0.03        23.70         0.10         0.03        23.84         2.17 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LI 
        1.45         1.58         1.48         1.35        20.78        81.96 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-PN-A8MA TCGA-UC-A7PF 
       19.33        15.58         2.96        93.99 

$`AMP PEAK 18(16P13.13) 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-A1MK 
       67.46        30.21        35.01        57.73        53.16         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       40.93         3.58        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-A3HL 
      100.14        38.43         0.82        52.01        18.02        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      182.93       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19        85.55        60.69        94.95         9.34        13.61 
TCGA-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-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR 
       16.83        16.18         7.33         0.76        12.36         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.82         0.62         1.18        14.50         1.35         1.35 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-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-EK-A2GZ TCGA-EK-A2H0 
        0.69        14.99        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ 
        6.64         0.53         0.59         0.07         0.36         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        2.24         0.10         0.07         0.10        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70         4.47         6.12         1.22         0.92 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        0.66         1.02         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.12        25.41        21.67        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LK 
      137.16        66.81       117.40        96.95        78.71        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 
       36.36        14.43        16.64        20.48        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.10         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         0.07         4.34         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        5.85         3.39         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       19.59         3.88        11.67 

  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                           0.03                            0.03 
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                          93.99                          182.93 
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                          14.73                           12.82 
[1] "0.0 - 94.0 (14.7)"  "0.0 - 182.9 (12.8)"
[1] "hr=" "1.3"
D18V2, continuous
                                 vv
clus                              T1 T2+T3+T4
  AMP PEAK 18(16P13.13) MUTATED   15       13
  AMP PEAK 18(16P13.13) WILD-TYPE 82       26
D18V3, multiclass
          clus
vv         AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  T1                                  15                              82
  T2+T3+T4                            13                              26
[1] 2 2
[1] FALSE
D18V4, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED   13 12
  AMP PEAK 18(16P13.13) WILD-TYPE 74 28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     13   12
  AMP PEAK 18(16P13.13) WILD-TYPE   74   28
   clus
vv  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  0                            13                              74
  1                            12                              28
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 18(16P13.13) MUTATED   13  1 13
  AMP PEAK 18(16P13.13) WILD-TYPE 59  2 52
D18V5, multiclass
    clus
vv   AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  M0                            13                              59
  M1                             1                               2
  MX                            13                              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 18(16P13.13) MUTATED               0
  AMP PEAK 18(16P13.13) WILD-TYPE             2
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(16P13.13) MUTATED                                 27
  AMP PEAK 18(16P13.13) WILD-TYPE                              117
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 18(16P13.13) MUTATED                                               1
  AMP PEAK 18(16P13.13) WILD-TYPE                                             3
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 18(16P13.13) MUTATED                                     5
  AMP PEAK 18(16P13.13) WILD-TYPE                                  15
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 18(16P13.13) MUTATED                                           0
  AMP PEAK 18(16P13.13) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 18(16P13.13) MUTATED                                              2
  AMP PEAK 18(16P13.13) WILD-TYPE                                            2
D18V6, multiclass
                                               clus
vv                                              AMP PEAK 18(16P13.13) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         27
  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                                              AMP PEAK 18(16P13.13) WILD-TYPE
  ADENOSQUAMOUS                                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          117
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        15
  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"
D18V7, binary
                                 cls
clus                                0   1
  AMP PEAK 18(16P13.13) MUTATED     6  29
  AMP PEAK 18(16P13.13) WILD-TYPE  21 120
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED      6   29
  AMP PEAK 18(16P13.13) WILD-TYPE   21  120
     clus
vv    AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  NO                              6                              21
  YES                            29                             120
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(16P13.13) MUTATED                                  3     2
  AMP PEAK 18(16P13.13) WILD-TYPE                                4    13
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(16P13.13) MUTATED                           2
  AMP PEAK 18(16P13.13) WILD-TYPE                        16
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 18(16P13.13) MUTATED                                           1
  AMP PEAK 18(16P13.13) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 18(16P13.13) MUTATED      23
  AMP PEAK 18(16P13.13) WILD-TYPE   107
D18V10, multiclass
                                           clus
vv                                          AMP PEAK 18(16P13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 2
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                23
                                           clus
vv                                          AMP PEAK 18(16P13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 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"
D18V11, binary
                                 cls
clus                                0   1
  AMP PEAK 18(16P13.13) MUTATED     2  23
  AMP PEAK 18(16P13.13) WILD-TYPE   9 104
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED      2   23
  AMP PEAK 18(16P13.13) WILD-TYPE    9  104
                        clus
vv                       AMP PEAK 18(16P13.13) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            23
                        clus
vv                       AMP PEAK 18(16P13.13) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             104
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED   10  7
  AMP PEAK 18(16P13.13) WILD-TYPE 38 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     10    7
  AMP PEAK 18(16P13.13) WILD-TYPE   38   12
            clus
vv           AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  TUMOR FREE                            10                              38
  WITH TUMOR                             7                              12
[1] 2 2
[1] FALSE
                                 vv
clus                              NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 18(16P13.13) MUTATED         1      1       1            30       2
  AMP PEAK 18(16P13.13) WILD-TYPE       0      9       5           117      10
D18V14, multiclass
               clus
vv              AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  NIGERIA                                   1                               0
  RUSSIA                                    1                               9
  UKRAINE                                   1                               5
  UNITED STATES                            30                             117
  VIETNAM                                   2                              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  AMP PEAK 18(16P13.13) MUTATED    2 18 15  0  0
  AMP PEAK 18(16P13.13) WILD-TYPE 12 65 57  1  5
D18V15, multiclass
    clus
vv   AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  G1                             2                              12
  G2                            18                              65
  G3                            15                              57
  G4                             0                               1
  GX                             0                               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V16, continuous
D18V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 18(16P13.13) MUTATED                                             2
  AMP PEAK 18(16P13.13) WILD-TYPE                                          19
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 18(16P13.13) MUTATED                                        2
  AMP PEAK 18(16P13.13) WILD-TYPE                                      6
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 18(16P13.13) MUTATED                                                 0
  AMP PEAK 18(16P13.13) WILD-TYPE                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 18(16P13.13) MUTATED               10                  14
  AMP PEAK 18(16P13.13) WILD-TYPE             26                  69
D18V18, multiclass
                                                 clus
vv                                                AMP PEAK 18(16P13.13) 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                                                             10
  LIFELONG NON-SMOKER                                                        14
                                                 clus
vv                                                AMP PEAK 18(16P13.13) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               26
  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"
D18V19, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 18(16P13.13) MUTATED             4        7             2        0
  AMP PEAK 18(16P13.13) WILD-TYPE          13       30             9        5
D18V20, multiclass
               clus
vv              AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  COMBINATION                               4                              13
  EXTERNAL                                  7                              30
  EXTERNAL BEAM                             2                               9
  INTERNAL                                  0                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V21, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED    1  0
  AMP PEAK 18(16P13.13) WILD-TYPE 10  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED      1    0
  AMP PEAK 18(16P13.13) WILD-TYPE   10    3
     clus
vv    AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  CGY                             1                              10
  GY                              0                               3
[1] 2 2
[1] FALSE
D18V22, continuous
D18V23, continuous
D18V24, continuous
D18V25, continuous
D18V26, continuous
D18V27, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 18(16P13.13) MUTATED                                     0
  AMP PEAK 18(16P13.13) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 18(16P13.13) MUTATED                                     1
  AMP PEAK 18(16P13.13) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 18(16P13.13) MUTATED                         1
  AMP PEAK 18(16P13.13) WILD-TYPE                       8
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 18(16P13.13) MUTATED                         0
  AMP PEAK 18(16P13.13) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 18(16P13.13) MUTATED                         1
  AMP PEAK 18(16P13.13) WILD-TYPE                       4
D18V28, multiclass
                                     clus
vv                                    AMP PEAK 18(16P13.13) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         1
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         1
                                     clus
vv                                    AMP PEAK 18(16P13.13) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                           8
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           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)
  AMP PEAK 18(16P13.13) MUTATED                                               0
  AMP PEAK 18(16P13.13) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 18(16P13.13) MUTATED                                                3
  AMP PEAK 18(16P13.13) WILD-TYPE                                              7
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 18(16P13.13) MUTATED                                                                                  12
  AMP PEAK 18(16P13.13) WILD-TYPE                                                                                42
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 18(16P13.13) MUTATED                                                                                             12
  AMP PEAK 18(16P13.13) WILD-TYPE                                                                                           65
D18V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 18(16P13.13) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            12
                                                                                              clus
vv                                                                                             AMP PEAK 18(16P13.13) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                             7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V30, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED   13 13
  AMP PEAK 18(16P13.13) WILD-TYPE 41 46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     13   13
  AMP PEAK 18(16P13.13) WILD-TYPE   41   46
         clus
vv        AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  ABSENT                             13                              41
  PRESENT                            13                              46
[1] 2 2
[1] FALSE
D18V31, continuous
D18V32, continuous
D18V33, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED    5 14
  AMP PEAK 18(16P13.13) WILD-TYPE 30 67
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED      5   14
  AMP PEAK 18(16P13.13) WILD-TYPE   30   67
                                          clus
vv                                         AMP PEAK 18(16P13.13) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            14
                                          clus
vv                                         AMP PEAK 18(16P13.13) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              67
[1] 2 2
[1] FALSE
D18V34, continuous
                                 vv
clus                              OTHER RADICAL HYSTERECTOMY
  AMP PEAK 18(16P13.13) MUTATED       0                   26
  AMP PEAK 18(16P13.13) WILD-TYPE     3                   87
                                 vv
clus                              SIMPLE HYSTERECTOMY
  AMP PEAK 18(16P13.13) MUTATED                     0
  AMP PEAK 18(16P13.13) WILD-TYPE                   5
D18V35, multiclass
                      clus
vv                     AMP PEAK 18(16P13.13) MUTATED
  OTHER                                            0
  RADICAL HYSTERECTOMY                            26
  SIMPLE HYSTERECTOMY                              0
                      clus
vv                     AMP PEAK 18(16P13.13) WILD-TYPE
  OTHER                                              3
  RADICAL HYSTERECTOMY                              87
  SIMPLE HYSTERECTOMY                                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 18(16P13.13) MUTATED              0           6          7
  AMP PEAK 18(16P13.13) WILD-TYPE            8          34         33
D18V36, multiclass
              clus
vv             AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  CURRENT USER                             0                               8
  FORMER USER                              6                              34
  NEVER USED                               7                              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V37, continuous
D18V38, binary
                                 cls
clus                               0  1
  AMP PEAK 18(16P13.13) MUTATED   11  5
  AMP PEAK 18(16P13.13) WILD-TYPE 62  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(16P13.13) MUTATED     11    5
  AMP PEAK 18(16P13.13) WILD-TYPE   62    9
         clus
vv        AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  ABSENT                             11                              62
  PRESENT                             5                               9
[1] 2 2
[1] FALSE
D18V39, continuous
[1] "Remove cluster labels:"        "AMP PEAK 18(16P13.13) MUTATED"
clus
  AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE 
                              2                               7 
                     TCGA-C5-A1BN                      TCGA-C5-A1MN 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-C5-A1MP                      TCGA-EK-A2RO 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-JW-A852                      TCGA-MU-A51Y 
"AMP PEAK 18(16P13.13) WILD-TYPE" "AMP PEAK 18(16P13.13) WILD-TYPE" 
                     TCGA-MU-A8JM 
"AMP PEAK 18(16P13.13) WILD-TYPE" 
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 18(16P13.13) MUTATED     0    0   1   10    4  0   2    3    1   6
  AMP PEAK 18(16P13.13) WILD-TYPE   2    1  21   41   17  3   4    3    7   7
                                 vv
clus                              T3B T4 TX
  AMP PEAK 18(16P13.13) MUTATED     1  0  1
  AMP PEAK 18(16P13.13) WILD-TYPE   1  1  6
D18V40, multiclass
      clus
vv     AMP PEAK 18(16P13.13) MUTATED AMP PEAK 18(16P13.13) WILD-TYPE
  T1A                              0                               2
  T1A1                             0                               1
  T1B                              1                              21
  T1B1                            10                              41
  T1B2                             4                              17
  T2                               0                               3
  T2A                              2                               4
  T2A1                             3                               3
  T2A2                             1                               7
  T2B                              6                               7
  T3B                              1                               1
  T4                               0                               1
  TX                               1                               6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V41, continuous

Clustering(19) Variable = AMP PEAK 19(17Q12) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(17Q12) MUTATED    24   6
  AMP PEAK 19(17Q12) WILD-TYPE 113  26
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          30                          139 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                           6                           26 
$`AMP PEAK 19(17Q12) 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-A7CO TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-DS-A0VM TCGA-DS-A3LQ 
       25.35        73.41        85.55         2.73       117.99        22.98 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A3HR TCGA-EA-A5ZF TCGA-EK-A2RD TCGA-EK-A2RM 
       16.18         7.33         1.32        14.96         0.03         2.24 
TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A40J TCGA-JW-A69B TCGA-LP-A4AU 
        0.10         6.94         6.12         1.35        10.06         0.10 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73R TCGA-UC-A7PF 
        0.82        13.87         3.45         5.85         6.25        93.99 

$`AMP PEAK 19(17Q12) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       67.46        46.32        30.21        57.73        53.16        38.99 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        0.46         2.43        40.93        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35        38.43         0.82        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       182.93       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
        9.67        17.19        60.69        94.95         9.34        13.61 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A5RQ 
       87.75        58.88        36.76         2.66       118.65        16.83 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28         0.76        12.36         1.74         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       13.91         0.69        14.99        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       45.96         6.64         0.53         0.59         0.07         4.04 
TCGA-EK-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-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A23K 
        0.03        20.35         7.92        14.70         4.47         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MU-A5YI 
       20.48        15.58         5.13         0.89         0.07         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96         3.72 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-R2-A69V TCGA-RA-A741 
        3.39         3.72         5.75         4.80        19.59         3.88 
TCGA-UC-A7PD 
       11.67 

  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                        0.03                         0.03 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                      117.99                       182.93 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                       8.695                       13.610 
[1] "0.0 - 118.0 (8.7)"  "0.0 - 182.9 (13.6)"
[1] "hr=" "1.2"
D19V2, continuous
                              vv
clus                           T1 T2+T3+T4
  AMP PEAK 19(17Q12) MUTATED   13        8
  AMP PEAK 19(17Q12) WILD-TYPE 84       31
D19V3, multiclass
          clus
vv         AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  T1                               13                           84
  T2+T3+T4                          8                           31
[1] 2 2
[1] FALSE
D19V4, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED   10  9
  AMP PEAK 19(17Q12) WILD-TYPE 77 31
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     10    9
  AMP PEAK 19(17Q12) WILD-TYPE   77   31
   clus
vv  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  0                         10                           77
  1                          9                           31
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  AMP PEAK 19(17Q12) MUTATED   13  0 11
  AMP PEAK 19(17Q12) WILD-TYPE 59  3 54
D19V5, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  M0                         13                           59
  M1                          0                            3
  MX                         11                           54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(17Q12) MUTATED               1                               22
  AMP PEAK 19(17Q12) WILD-TYPE             1                              122
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 19(17Q12) MUTATED                                               0
  AMP PEAK 19(17Q12) WILD-TYPE                                             4
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                                     7
  AMP PEAK 19(17Q12) WILD-TYPE                                  13
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 19(17Q12) MUTATED                                           0
  AMP PEAK 19(17Q12) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 19(17Q12) MUTATED                                              1
  AMP PEAK 19(17Q12) WILD-TYPE                                            3
D19V6, multiclass
                                               clus
vv                                              AMP PEAK 19(17Q12) MUTATED
  ADENOSQUAMOUS                                                          1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      22
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           1
                                               clus
vv                                              AMP PEAK 19(17Q12) WILD-TYPE
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       122
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     13
  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"
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED     4  27
  AMP PEAK 19(17Q12) WILD-TYPE  23 122
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      4   27
  AMP PEAK 19(17Q12) WILD-TYPE   23  122
     clus
vv    AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  NO                           4                           23
  YES                         27                          122
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(17Q12) MUTATED                                  1     3
  AMP PEAK 19(17Q12) WILD-TYPE                                6    12
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(17Q12) MUTATED                           1
  AMP PEAK 19(17Q12) WILD-TYPE                        17
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 19(17Q12) MUTATED                                           0    23
  AMP PEAK 19(17Q12) WILD-TYPE                                         1   107
D19V10, multiclass
                                           clus
vv                                          AMP PEAK 19(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              3
  BLACK OR AFRICAN AMERICAN                                          1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             23
                                           clus
vv                                          AMP PEAK 19(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     6
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                           17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              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"
D19V11, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED     3  21
  AMP PEAK 19(17Q12) WILD-TYPE   8 106
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      3   21
  AMP PEAK 19(17Q12) WILD-TYPE    8  106
                        clus
vv                       AMP PEAK 19(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         21
                        clus
vv                       AMP PEAK 19(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          106
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED    4  6
  AMP PEAK 19(17Q12) WILD-TYPE 44 13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      4    6
  AMP PEAK 19(17Q12) WILD-TYPE   44   13
            clus
vv           AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  TUMOR FREE                          4                           44
  WITH TUMOR                          6                           13
[1] 2 2
[1] FALSE
                              vv
clus                           NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 19(17Q12) MUTATED         0      1       0            27       3
  AMP PEAK 19(17Q12) WILD-TYPE       1      9       6           120       9
D19V14, multiclass
               clus
vv              AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  NIGERIA                                0                            1
  RUSSIA                                 1                            9
  UKRAINE                                0                            6
  UNITED STATES                         27                          120
  VIETNAM                                3                            9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           G1 G2 G3 G4 GX
  AMP PEAK 19(17Q12) MUTATED    0 14 15  0  2
  AMP PEAK 19(17Q12) WILD-TYPE 14 69 57  1  3
D19V15, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  G1                          0                           14
  G2                         14                           69
  G3                         15                           57
  G4                          0                            1
  GX                          2                            3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V16, continuous
D19V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 19(17Q12) MUTATED                                             1
  AMP PEAK 19(17Q12) WILD-TYPE                                          20
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 19(17Q12) MUTATED                                        2
  AMP PEAK 19(17Q12) WILD-TYPE                                      6
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 19(17Q12) MUTATED                                                 0
  AMP PEAK 19(17Q12) WILD-TYPE                                               1
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 19(17Q12) MUTATED                6                  18
  AMP PEAK 19(17Q12) WILD-TYPE             30                  65
D19V18, multiclass
                                                 clus
vv                                                AMP PEAK 19(17Q12) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          0
  CURRENT SMOKER                                                           6
  LIFELONG NON-SMOKER                                                     18
                                                 clus
vv                                                AMP PEAK 19(17Q12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            30
  LIFELONG NON-SMOKER                                                       65
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V19, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 19(17Q12) MUTATED             2        7             2        1
  AMP PEAK 19(17Q12) WILD-TYPE          15       30             9        4
D19V20, multiclass
               clus
vv              AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  COMBINATION                            2                           15
  EXTERNAL                               7                           30
  EXTERNAL BEAM                          2                            9
  INTERNAL                               1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V21, binary
                              cls
clus                           0 1
  AMP PEAK 19(17Q12) MUTATED   3 0
  AMP PEAK 19(17Q12) WILD-TYPE 8 3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      3    0
  AMP PEAK 19(17Q12) WILD-TYPE    8    3
     clus
vv    AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  CGY                          3                            8
  GY                           0                            3
[1] 2 2
[1] FALSE
D19V22, continuous
D19V23, continuous
D19V24, continuous
D19V25, continuous
D19V26, continuous
D19V27, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 19(17Q12) MUTATED                                     0
  AMP PEAK 19(17Q12) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 19(17Q12) MUTATED                                     1
  AMP PEAK 19(17Q12) WILD-TYPE                                   5
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 19(17Q12) MUTATED                         2                       0
  AMP PEAK 19(17Q12) WILD-TYPE                       7                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  AMP PEAK 19(17Q12) MUTATED                         0
  AMP PEAK 19(17Q12) WILD-TYPE                       5
D19V28, multiclass
                                     clus
vv                                    AMP PEAK 19(17Q12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          1
  OTHER LOCATION, SPECIFY                                      2
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      0
                                     clus
vv                                    AMP PEAK 19(17Q12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            5
  OTHER LOCATION, SPECIFY                                        7
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        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)
  AMP PEAK 19(17Q12) MUTATED                                               0
  AMP PEAK 19(17Q12) WILD-TYPE                                             2
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 19(17Q12) MUTATED                                                2
  AMP PEAK 19(17Q12) WILD-TYPE                                              8
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 19(17Q12) MUTATED                                                                                  10
  AMP PEAK 19(17Q12) WILD-TYPE                                                                                44
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 19(17Q12) MUTATED                                                                                             13
  AMP PEAK 19(17Q12) WILD-TYPE                                                                                           64
D19V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 19(17Q12) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                         0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                        2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                    10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         13
                                                                                              clus
vv                                                                                             AMP PEAK 19(17Q12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      44
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V30, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED    6 12
  AMP PEAK 19(17Q12) WILD-TYPE 48 47
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      6   12
  AMP PEAK 19(17Q12) WILD-TYPE   48   47
         clus
vv        AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  ABSENT                           6                           48
  PRESENT                         12                           47
[1] 2 2
[1] FALSE
D19V31, continuous
D19V32, continuous
D19V33, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED    2 14
  AMP PEAK 19(17Q12) WILD-TYPE 33 67
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      2   14
  AMP PEAK 19(17Q12) WILD-TYPE   33   67
                                          clus
vv                                         AMP PEAK 19(17Q12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              2
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         14
                                          clus
vv                                         AMP PEAK 19(17Q12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           67
[1] 2 2
[1] FALSE
D19V34, continuous
                              vv
clus                           OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 19(17Q12) MUTATED       0                   18                   1
  AMP PEAK 19(17Q12) WILD-TYPE     3                   95                   4
D19V35, multiclass
                      clus
vv                     AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  OTHER                                         0                            3
  RADICAL HYSTERECTOMY                         18                           95
  SIMPLE HYSTERECTOMY                           1                            4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  AMP PEAK 19(17Q12) MUTATED              2           8          5
  AMP PEAK 19(17Q12) WILD-TYPE            6          32         35
D19V36, multiclass
              clus
vv             AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  CURRENT USER                          2                            6
  FORMER USER                           8                           32
  NEVER USED                            5                           35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V37, continuous
D19V38, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED   10  2
  AMP PEAK 19(17Q12) WILD-TYPE 63 12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     10    2
  AMP PEAK 19(17Q12) WILD-TYPE   63   12
         clus
vv        AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  ABSENT                          10                           63
  PRESENT                          2                           12
[1] 2 2
[1] FALSE
D19V39, continuous
[1] "Remove cluster labels:"     "AMP PEAK 19(17Q12) MUTATED"
clus
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                           2                            7 
                  TCGA-C5-A1BN                   TCGA-C5-A1MH 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-C5-A1MN                   TCGA-EK-A2RO 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-HM-A3JK                   TCGA-JW-A852 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-MU-A8JM 
"AMP PEAK 19(17Q12) WILD-TYPE" 
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK 19(17Q12) MUTATED     1    0   0    8    4  1   2    3    0   0   2
  AMP PEAK 19(17Q12) WILD-TYPE   1    1  22   43   17  2   4    3    8  13   0
                              vv
clus                           T4 TX
  AMP PEAK 19(17Q12) MUTATED    0  3
  AMP PEAK 19(17Q12) WILD-TYPE  1  4
D19V40, multiclass
      clus
vv     AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  T1A                           1                            1
  T1A1                          0                            1
  T1B                           0                           22
  T1B1                          8                           43
  T1B2                          4                           17
  T2                            1                            2
  T2A                           2                            4
  T2A1                          3                            3
  T2A2                          0                            8
  T2B                           0                           13
  T3B                           2                            0
  T4                            0                            1
  TX                            3                            4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V41, continuous

Clustering(20) Variable = AMP PEAK 20(17Q25.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(17Q25.1) MUTATED    35   8
  AMP PEAK 20(17Q25.1) WILD-TYPE 102  24
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            43                            126 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                             8                             24 
$`AMP PEAK 20(17Q25.1) MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MP 
       23.67        31.40        35.01        53.16        35.61         3.58 
TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE 
      100.14        25.35       134.33         9.67        73.41        85.55 
TCGA-C5-A7X5 TCGA-DS-A0VK TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3QD 
       13.61        36.76        22.98         1.74         1.32        13.05 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2RD 
       14.50        14.89        13.91        14.96         6.64         0.03 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A3HY TCGA-FU-A3NI 
        2.24         0.10         6.94         6.12         0.66         1.45 
TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-JW-A5VI 
        1.58         1.35        14.93       147.39       117.40        16.64 
TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A51Y TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       10.06         0.10         0.89        13.87         3.45         5.85 
TCGA-UC-A7PF 
       93.99 

$`AMP PEAK 20(17Q25.1) 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-A1MH TCGA-C5-A1MJ 
       67.46        46.32        30.21        57.73        38.99         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
        2.43        40.93        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UH 
       20.42       182.93       101.82        15.48        17.19        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       94.95         9.34         2.73        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99       118.65        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 
        0.76        12.36         0.82         0.62         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
        1.48         0.69        14.99        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
       45.96         0.53         0.59         0.07         4.04         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-FU-A23K TCGA-FU-A23L 
       20.35         7.92        14.70         4.47         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.92         2.17         1.02         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
        4.11       137.16        66.81        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        36.36        14.43        19.33        20.48        15.58 
TCGA-JW-A852 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        5.13         0.07         0.82         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         3.72         3.39         3.72 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.75         4.80         6.25        19.59         3.88        11.67 

  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                        147.39                         182.93 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                         13.87                          13.15 
[1] "0.0 - 147.4 (13.9)" "0.0 - 182.9 (13.2)"
[1] "hr=" "1"  
D20V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK 20(17Q25.1) MUTATED   21       11
  AMP PEAK 20(17Q25.1) WILD-TYPE 76       28
D20V3, multiclass
          clus
vv         AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  T1                                 21                             76
  T2+T3+T4                           11                             28
[1] 2 2
[1] FALSE
D20V4, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED   16 13
  AMP PEAK 20(17Q25.1) WILD-TYPE 71 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     16   13
  AMP PEAK 20(17Q25.1) WILD-TYPE   71   27
   clus
vv  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  0                           16                             71
  1                           13                             27
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 20(17Q25.1) MUTATED   19  0 15
  AMP PEAK 20(17Q25.1) WILD-TYPE 53  3 50
D20V5, multiclass
    clus
vv   AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  M0                           19                             53
  M1                            0                              3
  MX                           15                             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(17Q25.1) MUTATED               0                               39
  AMP PEAK 20(17Q25.1) WILD-TYPE             2                              105
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 20(17Q25.1) MUTATED                                               1
  AMP PEAK 20(17Q25.1) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 20(17Q25.1) MUTATED                                     5
  AMP PEAK 20(17Q25.1) WILD-TYPE                                  15
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 20(17Q25.1) MUTATED                                           1
  AMP PEAK 20(17Q25.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 20(17Q25.1) MUTATED                                              0
  AMP PEAK 20(17Q25.1) WILD-TYPE                                            4
D20V6, multiclass
                                               clus
vv                                              AMP PEAK 20(17Q25.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        39
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              AMP PEAK 20(17Q25.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         105
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       15
  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"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q25.1) MUTATED     5  41
  AMP PEAK 20(17Q25.1) WILD-TYPE  22 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED      5   41
  AMP PEAK 20(17Q25.1) WILD-TYPE   22  108
     clus
vv    AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  NO                             5                             22
  YES                           41                            108
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(17Q25.1) MUTATED                                  2     4
  AMP PEAK 20(17Q25.1) WILD-TYPE                                5    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(17Q25.1) MUTATED                           2
  AMP PEAK 20(17Q25.1) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 20(17Q25.1) MUTATED                                           0
  AMP PEAK 20(17Q25.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 20(17Q25.1) MUTATED      36
  AMP PEAK 20(17Q25.1) WILD-TYPE    94
D20V10, multiclass
                                           clus
vv                                          AMP PEAK 20(17Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               36
                                           clus
vv                                          AMP PEAK 20(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 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"
D20V11, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED    4 30
  AMP PEAK 20(17Q25.1) WILD-TYPE  7 97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED      4   30
  AMP PEAK 20(17Q25.1) WILD-TYPE    7   97
                        clus
vv                       AMP PEAK 20(17Q25.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       AMP PEAK 20(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             97
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED   11  5
  AMP PEAK 20(17Q25.1) WILD-TYPE 37 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     11    5
  AMP PEAK 20(17Q25.1) WILD-TYPE   37   14
            clus
vv           AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  TUMOR FREE                           11                             37
  WITH TUMOR                            5                             14
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 20(17Q25.1) MUTATED         0      3       1            38       4
  AMP PEAK 20(17Q25.1) WILD-TYPE       1      7       5           109       8
D20V14, multiclass
               clus
vv              AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   3                              7
  UKRAINE                                  1                              5
  UNITED STATES                           38                            109
  VIETNAM                                  4                              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 20(17Q25.1) MUTATED    1 21 23  0  1
  AMP PEAK 20(17Q25.1) WILD-TYPE 13 62 49  1  4
D20V15, multiclass
    clus
vv   AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  G1                            1                             13
  G2                           21                             62
  G3                           23                             49
  G4                            0                              1
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V16, continuous
D20V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 20(17Q25.1) MUTATED                                             5
  AMP PEAK 20(17Q25.1) WILD-TYPE                                          16
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 20(17Q25.1) MUTATED                                        3
  AMP PEAK 20(17Q25.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 20(17Q25.1) MUTATED                                                 1
  AMP PEAK 20(17Q25.1) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 20(17Q25.1) MUTATED                9                  20
  AMP PEAK 20(17Q25.1) WILD-TYPE             27                  63
D20V18, multiclass
                                                 clus
vv                                                AMP PEAK 20(17Q25.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             9
  LIFELONG NON-SMOKER                                                       20
                                                 clus
vv                                                AMP PEAK 20(17Q25.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                              27
  LIFELONG NON-SMOKER                                                         63
[1] 5 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
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 20(17Q25.1) MUTATED             3       14             3        1
  AMP PEAK 20(17Q25.1) WILD-TYPE          14       23             8        4
D20V20, multiclass
               clus
vv              AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  COMBINATION                              3                             14
  EXTERNAL                                14                             23
  EXTERNAL BEAM                            3                              8
  INTERNAL                                 1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V21, binary
                                cls
clus                             0 1
  AMP PEAK 20(17Q25.1) MUTATED   4 0
  AMP PEAK 20(17Q25.1) WILD-TYPE 7 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED      4    0
  AMP PEAK 20(17Q25.1) WILD-TYPE    7    3
     clus
vv    AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  CGY                            4                              7
  GY                             0                              3
[1] 2 2
[1] FALSE
D20V22, continuous
D20V23, continuous
D20V24, continuous
D20V25, continuous
D20V26, continuous
D20V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 20(17Q25.1) MUTATED                                     0
  AMP PEAK 20(17Q25.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 20(17Q25.1) MUTATED                                     1
  AMP PEAK 20(17Q25.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 20(17Q25.1) MUTATED                         2
  AMP PEAK 20(17Q25.1) WILD-TYPE                       7
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 20(17Q25.1) MUTATED                         0
  AMP PEAK 20(17Q25.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 20(17Q25.1) MUTATED                         1
  AMP PEAK 20(17Q25.1) WILD-TYPE                       4
D20V28, multiclass
                                     clus
vv                                    AMP PEAK 20(17Q25.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        2
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 20(17Q25.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          7
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  AMP PEAK 20(17Q25.1) MUTATED                                               0
  AMP PEAK 20(17Q25.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 20(17Q25.1) MUTATED                                                3
  AMP PEAK 20(17Q25.1) WILD-TYPE                                              7
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 20(17Q25.1) MUTATED                                                                                  13
  AMP PEAK 20(17Q25.1) WILD-TYPE                                                                                41
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 20(17Q25.1) MUTATED                                                                                             20
  AMP PEAK 20(17Q25.1) WILD-TYPE                                                                                           57
D20V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 20(17Q25.1) 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                                                                                             AMP PEAK 20(17Q25.1) 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)                                        41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V30, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED    8 18
  AMP PEAK 20(17Q25.1) WILD-TYPE 46 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED      8   18
  AMP PEAK 20(17Q25.1) WILD-TYPE   46   41
         clus
vv        AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  ABSENT                             8                             46
  PRESENT                           18                             41
[1] 2 2
[1] FALSE
D20V31, continuous
D20V32, continuous
D20V33, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED    9 18
  AMP PEAK 20(17Q25.1) WILD-TYPE 26 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED      9   18
  AMP PEAK 20(17Q25.1) WILD-TYPE   26   63
                                          clus
vv                                         AMP PEAK 20(17Q25.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           18
                                          clus
vv                                         AMP PEAK 20(17Q25.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             63
[1] 2 2
[1] FALSE
D20V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 20(17Q25.1) MUTATED       0                   28                   1
  AMP PEAK 20(17Q25.1) WILD-TYPE     3                   85                   4
D20V35, multiclass
                      clus
vv                     AMP PEAK 20(17Q25.1) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           28
  SIMPLE HYSTERECTOMY                             1
                      clus
vv                     AMP PEAK 20(17Q25.1) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             85
  SIMPLE HYSTERECTOMY                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 20(17Q25.1) MUTATED              3          12          7
  AMP PEAK 20(17Q25.1) WILD-TYPE            5          28         33
D20V36, multiclass
              clus
vv             AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  CURRENT USER                            3                              5
  FORMER USER                            12                             28
  NEVER USED                              7                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V37, continuous
D20V38, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.1) MUTATED   16  4
  AMP PEAK 20(17Q25.1) WILD-TYPE 57 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.1) MUTATED     16    4
  AMP PEAK 20(17Q25.1) WILD-TYPE   57   10
         clus
vv        AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  ABSENT                            16                             57
  PRESENT                            4                             10
[1] 2 2
[1] FALSE
D20V39, continuous
[1] "Remove cluster labels:"       "AMP PEAK 20(17Q25.1) MUTATED"
clus
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"AMP PEAK 20(17Q25.1) WILD-TYPE" "AMP PEAK 20(17Q25.1) WILD-TYPE" 
                    TCGA-C5-A1MN                     TCGA-EK-A2RO 
"AMP PEAK 20(17Q25.1) WILD-TYPE" "AMP PEAK 20(17Q25.1) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"AMP PEAK 20(17Q25.1) WILD-TYPE" "AMP PEAK 20(17Q25.1) WILD-TYPE" 
                    TCGA-MU-A8JM 
"AMP PEAK 20(17Q25.1) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 20(17Q25.1) MUTATED     1    0   0   13    7  1   2    4    0   2
  AMP PEAK 20(17Q25.1) WILD-TYPE   1    1  22   38   14  2   4    2    8  11
                                vv
clus                             T3B T4 TX
  AMP PEAK 20(17Q25.1) MUTATED     2  0  2
  AMP PEAK 20(17Q25.1) WILD-TYPE   0  1  5
D20V40, multiclass
      clus
vv     AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             0                             22
  T1B1                           13                             38
  T1B2                            7                             14
  T2                              1                              2
  T2A                             2                              4
  T2A1                            4                              2
  T2A2                            0                              8
  T2B                             2                             11
  T3B                             2                              0
  T4                              0                              1
  TX                              2                              5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V41, continuous

Clustering(21) Variable = AMP PEAK 21(19Q13.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(19Q13.2) MUTATED    36  13
  AMP PEAK 21(19Q13.2) WILD-TYPE 101  19
  AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE 
                            49                            120 
  AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE 
                            13                             19 
$`AMP PEAK 21(19Q13.2) MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1ME 
       23.67        11.44       144.16         5.46        31.40        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A2LT TCGA-C5-A2LY 
       53.16        38.99        35.61         2.43        73.18        78.35 
TCGA-C5-A2M1 TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7CO 
       38.43       182.93        25.35       134.33         9.67        73.41 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HR 
        9.34        13.61         2.66        22.98         8.28         1.32 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 
       14.50         1.35        14.50         1.81         0.26        13.91 
TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-FU-A23L 
       14.96         0.59         1.18         2.24         0.10        23.84 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LH TCGA-IR-A3LK 
        1.45         1.35        21.67        20.78        78.71        26.56 
TCGA-IR-A3LL TCGA-JW-A5VI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 
       36.36        16.64        29.72         0.07         2.96         5.85 
TCGA-Q1-A6DT 
        3.39 

$`AMP PEAK 21(19Q13.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK 
       49.48        57.04        68.84        18.74        36.56       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-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
       35.01         0.46        40.93         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       83.05       100.14         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       20.42       101.82        15.48        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       94.95         2.73        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         7.33         0.76        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-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.66        12.82        14.89         1.48         0.69        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.58        13.48        12.59        45.96         6.64         0.53 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO 
        0.07         4.04         0.03         0.36        23.70         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         4.47         6.12         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.32         1.97         1.12        25.41        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
      147.39       137.16        66.81       117.40        96.95        81.96 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       14.43        19.33        20.48        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.10         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        5.42         4.34         3.72         3.45         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE 
                        182.93                         177.04 
  AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE 
                         14.50                          12.74 
[1] "0.1 - 182.9 (14.5)" "0.0 - 177.0 (12.7)"
[1] "hr=" "1.6"
D21V2, continuous
                                vv
clus                             T1 T2+T3+T4
  AMP PEAK 21(19Q13.2) MUTATED   22       13
  AMP PEAK 21(19Q13.2) WILD-TYPE 75       26
D21V3, multiclass
          clus
vv         AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  T1                                 22                             75
  T2+T3+T4                           13                             26
[1] 2 2
[1] FALSE
D21V4, binary
                                cls
clus                              0  1
  AMP PEAK 21(19Q13.2) MUTATED   22 11
  AMP PEAK 21(19Q13.2) WILD-TYPE 65 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19Q13.2) MUTATED     22   11
  AMP PEAK 21(19Q13.2) WILD-TYPE   65   29
   clus
vv  AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  0                           22                             65
  1                           11                             29
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 21(19Q13.2) MUTATED   21  0 16
  AMP PEAK 21(19Q13.2) WILD-TYPE 51  3 49
D21V5, multiclass
    clus
vv   AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  M0                           21                             51
  M1                            0                              3
  MX                           16                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(19Q13.2) MUTATED               0                               48
  AMP PEAK 21(19Q13.2) WILD-TYPE             2                               96
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 21(19Q13.2) MUTATED                                               1
  AMP PEAK 21(19Q13.2) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 21(19Q13.2) MUTATED                                     4
  AMP PEAK 21(19Q13.2) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 21(19Q13.2) MUTATED                                           0
  AMP PEAK 21(19Q13.2) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 21(19Q13.2) MUTATED                                              0
  AMP PEAK 21(19Q13.2) WILD-TYPE                                            4
D21V6, multiclass
                                               clus
vv                                              AMP PEAK 21(19Q13.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        48
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              AMP PEAK 21(19Q13.2) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          96
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  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"
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(19Q13.2) MUTATED    13  40
  AMP PEAK 21(19Q13.2) WILD-TYPE  14 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19Q13.2) MUTATED     13   40
  AMP PEAK 21(19Q13.2) WILD-TYPE   14  109
     clus
vv    AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  NO                            13                             14
  YES                           40                            109
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(19Q13.2) MUTATED                                  1     3
  AMP PEAK 21(19Q13.2) WILD-TYPE                                6    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(19Q13.2) MUTATED                           6
  AMP PEAK 21(19Q13.2) WILD-TYPE                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 21(19Q13.2) MUTATED                                           0
  AMP PEAK 21(19Q13.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 21(19Q13.2) MUTATED      42
  AMP PEAK 21(19Q13.2) WILD-TYPE    88
D21V10, multiclass
                                           clus
vv                                          AMP PEAK 21(19Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               42
                                           clus
vv                                          AMP PEAK 21(19Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 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"
D21V11, binary
                                cls
clus                              0  1
  AMP PEAK 21(19Q13.2) MUTATED    4 37
  AMP PEAK 21(19Q13.2) WILD-TYPE  7 90
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19Q13.2) MUTATED      4   37
  AMP PEAK 21(19Q13.2) WILD-TYPE    7   90
                        clus
vv                       AMP PEAK 21(19Q13.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       AMP PEAK 21(19Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             90
[1] 2 2
[1] FALSE
D21V12, continuous
D21V13, binary
                                cls
clus                              0  1
  AMP PEAK 21(19Q13.2) MUTATED   14 11
  AMP PEAK 21(19Q13.2) WILD-TYPE 34  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19Q13.2) MUTATED     14   11
  AMP PEAK 21(19Q13.2) WILD-TYPE   34    8
            clus
vv           AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  TUMOR FREE                           14                             34
  WITH TUMOR                           11                              8
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 21(19Q13.2) MUTATED         1      2       3            44       3
  AMP PEAK 21(19Q13.2) WILD-TYPE       0      8       3           103       9
D21V14, multiclass
               clus
vv              AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  NIGERIA                                  1                              0
  RUSSIA                                   2                              8
  UKRAINE                                  3                              3
  UNITED STATES                           44                            103
  VIETNAM                                  3                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  AMP PEAK 21(19Q13.2) MUTATED    2 24 24  1  1
  AMP PEAK 21(19Q13.2) WILD-TYPE 12 59 48  0  4
D21V15, multiclass
    clus
vv   AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  G1                            2                             12
  G2                           24                             59
  G3                           24                             48
  G4                            1                              0
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V16, continuous
D21V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 21(19Q13.2) MUTATED                                             6
  AMP PEAK 21(19Q13.2) WILD-TYPE                                          15
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 21(19Q13.2) MUTATED                                        3
  AMP PEAK 21(19Q13.2) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 21(19Q13.2) MUTATED                                                 1
  AMP PEAK 21(19Q13.2) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 21(19Q13.2) MUTATED                5                  27
  AMP PEAK 21(19Q13.2) WILD-TYPE             31                  56
D21V18, multiclass
                                                 clus
vv                                                AMP PEAK 21(19Q13.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             5
  LIFELONG NON-SMOKER                                                       27
                                                 clus
vv                                                AMP PEAK 21(19Q13.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                              31
  LIFELONG NON-SMOKER                                                         56
[1] 5 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
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 21(19Q13.2) MUTATED             8       14             5        1
  AMP PEAK 21(19Q13.2) WILD-TYPE           9       23             6        4
D21V20, multiclass
               clus
vv              AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  COMBINATION                              8                              9
  EXTERNAL                                14                             23
  EXTERNAL BEAM                            5                              6
  INTERNAL                                 1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V21, binary
                                cls
clus                             0 1
  AMP PEAK 21(19Q13.2) MUTATED   6 0
  AMP PEAK 21(19Q13.2) WILD-TYPE 5 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19Q13.2) MUTATED      6    0
  AMP PEAK 21(19Q13.2) WILD-TYPE    5    3
     clus
vv    AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  CGY                            6                              5
  GY                             0                              3
[1] 2 2
[1] FALSE
D21V22, continuous
D21V23, continuous
D21V24, continuous
D21V25, continuous
D21V26, continuous
D21V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 21(19Q13.2) MUTATED                                     0
  AMP PEAK 21(19Q13.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 21(19Q13.2) MUTATED                                     3
  AMP PEAK 21(19Q13.2) WILD-TYPE                                   3
                                vv
clus                             OTHER LOCATION, SPECIFY
  AMP PEAK 21(19Q13.2) MUTATED                         3
  AMP PEAK 21(19Q13.2) WILD-TYPE                       6
                                vv
clus                             POSITIVE BLADDER MARGIN
  AMP PEAK 21(19Q13.2) MUTATED                         1
  AMP PEAK 21(19Q13.2) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  AMP PEAK 21(19Q13.2) MUTATED                         1
  AMP PEAK 21(19Q13.2) WILD-TYPE                       4
D21V28, multiclass
                                     clus
vv                                    AMP PEAK 21(19Q13.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                        3
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    AMP PEAK 21(19Q13.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              3
  OTHER LOCATION, SPECIFY                                          6
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          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)
  AMP PEAK 21(19Q13.2) MUTATED                                               0
  AMP PEAK 21(19Q13.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 21(19Q13.2) MUTATED                                                2
  AMP PEAK 21(19Q13.2) WILD-TYPE                                              8
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 21(19Q13.2) MUTATED                                                                                  17
  AMP PEAK 21(19Q13.2) WILD-TYPE                                                                                37
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 21(19Q13.2) MUTATED                                                                                             23
  AMP PEAK 21(19Q13.2) WILD-TYPE                                                                                           54
D21V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 21(19Q13.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           23
                                                                                              clus
vv                                                                                             AMP PEAK 21(19Q13.2) 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)                                        37
  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"
D21V30, binary
                                cls
clus                              0  1
  AMP PEAK 21(19Q13.2) MUTATED   15 18
  AMP PEAK 21(19Q13.2) WILD-TYPE 39 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19Q13.2) MUTATED     15   18
  AMP PEAK 21(19Q13.2) WILD-TYPE   39   41
         clus
vv        AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  ABSENT                            15                             39
  PRESENT                           18                             41
[1] 2 2
[1] FALSE
D21V31, continuous
D21V32, continuous
D21V33, binary
                                cls
clus                              0  1
  AMP PEAK 21(19Q13.2) MUTATED   13 22
  AMP PEAK 21(19Q13.2) WILD-TYPE 22 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19Q13.2) MUTATED     13   22
  AMP PEAK 21(19Q13.2) WILD-TYPE   22   59
                                          clus
vv                                         AMP PEAK 21(19Q13.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           22
                                          clus
vv                                         AMP PEAK 21(19Q13.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             59
[1] 2 2
[1] FALSE
D21V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 21(19Q13.2) MUTATED       0                   31                   1
  AMP PEAK 21(19Q13.2) WILD-TYPE     3                   82                   4
D21V35, multiclass
                      clus
vv                     AMP PEAK 21(19Q13.2) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           31
  SIMPLE HYSTERECTOMY                             1
                      clus
vv                     AMP PEAK 21(19Q13.2) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             82
  SIMPLE HYSTERECTOMY                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  AMP PEAK 21(19Q13.2) MUTATED              2          14         10
  AMP PEAK 21(19Q13.2) WILD-TYPE            6          26         30
D21V36, multiclass
              clus
vv             AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                            14                             26
  NEVER USED                             10                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V37, continuous
D21V38, binary
                                cls
clus                              0  1
  AMP PEAK 21(19Q13.2) MUTATED   18  5
  AMP PEAK 21(19Q13.2) WILD-TYPE 55  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19Q13.2) MUTATED     18    5
  AMP PEAK 21(19Q13.2) WILD-TYPE   55    9
         clus
vv        AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  ABSENT                            18                             55
  PRESENT                            5                              9
[1] 2 2
[1] FALSE
D21V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 21(19Q13.2) MUTATED     0    0   4   14    4  0   1    4    1   5
  AMP PEAK 21(19Q13.2) WILD-TYPE   2    1  18   37   17  3   5    2    7   8
                                vv
clus                             T3B T4 TX
  AMP PEAK 21(19Q13.2) MUTATED     1  1  2
  AMP PEAK 21(19Q13.2) WILD-TYPE   1  0  5
D21V40, multiclass
      clus
vv     AMP PEAK 21(19Q13.2) MUTATED AMP PEAK 21(19Q13.2) WILD-TYPE
  T1A                             0                              2
  T1A1                            0                              1
  T1B                             4                             18
  T1B1                           14                             37
  T1B2                            4                             17
  T2                              0                              3
  T2A                             1                              5
  T2A1                            4                              2
  T2A2                            1                              7
  T2B                             5                              8
  T3B                             1                              1
  T4                              1                              0
  TX                              2                              5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V41, continuous

Clustering(22) Variable = AMP PEAK 22(20Q11.21) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 22(20Q11.21) MUTATED   60 12
  AMP PEAK 22(20Q11.21) WILD-TYPE 77 20
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                             72                              97 
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                             12                              20 
$`AMP PEAK 22(20Q11.21) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BL 
       49.48        57.04        23.67        68.84       144.16       173.29 
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       31.40        35.01        57.73        35.61         0.46         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A7CG 
       40.93         3.58        44.22        73.18       100.14       182.93 
TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 
       25.35         9.67        73.41        17.19        60.69        13.61 
TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT 
        2.73        36.76        22.98         7.33         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A556 
        1.74         1.32         0.82        13.05        14.50        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG 
        1.48        14.96        13.58        12.59        45.96         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EK-A3GN TCGA-FU-A23K 
        0.59         1.18         2.24         0.10         0.03         1.22 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A40J TCGA-HG-A2PA 
       23.84         2.17         0.66         1.45         1.35        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JW-A5VK 
       21.67        20.78       147.39        96.95        78.71        20.48 
TCGA-JW-A69B TCGA-LP-A4AX TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       10.06         0.07         0.03         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-RA-A741 TCGA-UC-A7PF 
        5.85         3.39         5.75         4.80         3.88        93.99 

$`AMP PEAK 22(20Q11.21) WILD-TYPE`
TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN 
       11.44        18.74        36.56       177.04        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-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-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-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       85.55        94.95         9.34        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3HT 
      117.99       118.65        16.83        16.18         8.28         0.62 
TCGA-EA-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-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R 
       12.82         0.26        13.91         0.69        14.99        13.48 
TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        6.64         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.07         0.10        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A3TQ 
       14.70         4.47         6.12         0.92         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-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI 
       14.93         4.11       137.16        66.81       117.40        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       26.56        36.36        14.43        16.64        19.33        15.58 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM 
        5.13         0.10         0.89         0.82        13.87         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73R TCGA-R2-A69V 
       29.72         0.07         4.34         3.72         6.25        19.59 
TCGA-UC-A7PD 
       11.67 

  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                           0.03                            0.03 
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                         182.93                          177.04 
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                         13.315                          13.870 
[1] "0.0 - 182.9 (13.3)" "0.0 - 177.0 (13.9)"
[1] "hr=" "1.3"
D22V2, continuous
                                 vv
clus                              T1 T2+T3+T4
  AMP PEAK 22(20Q11.21) MUTATED   40       13
  AMP PEAK 22(20Q11.21) WILD-TYPE 57       26
D22V3, multiclass
          clus
vv         AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  T1                                  40                              57
  T2+T3+T4                            13                              26
[1] 2 2
[1] FALSE
D22V4, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.21) MUTATED   30 19
  AMP PEAK 22(20Q11.21) WILD-TYPE 57 21
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED     30   19
  AMP PEAK 22(20Q11.21) WILD-TYPE   57   21
   clus
vv  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  0                            30                              57
  1                            19                              21
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 22(20Q11.21) MUTATED   33  0 24
  AMP PEAK 22(20Q11.21) WILD-TYPE 39  3 41
D22V5, multiclass
    clus
vv   AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  M0                            33                              39
  M1                             0                               3
  MX                            24                              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  AMP PEAK 22(20Q11.21) MUTATED               0
  AMP PEAK 22(20Q11.21) WILD-TYPE             2
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(20Q11.21) MUTATED                                 60
  AMP PEAK 22(20Q11.21) WILD-TYPE                               84
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 22(20Q11.21) MUTATED                                               3
  AMP PEAK 22(20Q11.21) WILD-TYPE                                             1
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 22(20Q11.21) MUTATED                                    10
  AMP PEAK 22(20Q11.21) WILD-TYPE                                  10
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 22(20Q11.21) MUTATED                                           1
  AMP PEAK 22(20Q11.21) WILD-TYPE                                         1
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 22(20Q11.21) MUTATED                                              2
  AMP PEAK 22(20Q11.21) WILD-TYPE                                            2
D22V6, multiclass
                                               clus
vv                                              AMP PEAK 22(20Q11.21) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         60
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              2
                                               clus
vv                                              AMP PEAK 22(20Q11.21) WILD-TYPE
  ADENOSQUAMOUS                                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                                           84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               1
  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"
D22V7, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.21) MUTATED   12 64
  AMP PEAK 22(20Q11.21) WILD-TYPE 15 85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED     12   64
  AMP PEAK 22(20Q11.21) WILD-TYPE   15   85
     clus
vv    AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  NO                             12                              15
  YES                            64                              85
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(20Q11.21) MUTATED                                  0     5
  AMP PEAK 22(20Q11.21) WILD-TYPE                                7    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(20Q11.21) MUTATED                           9
  AMP PEAK 22(20Q11.21) WILD-TYPE                         9
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 22(20Q11.21) MUTATED                                           0
  AMP PEAK 22(20Q11.21) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 22(20Q11.21) MUTATED      60
  AMP PEAK 22(20Q11.21) WILD-TYPE    70
D22V10, multiclass
                                           clus
vv                                          AMP PEAK 22(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                60
                                           clus
vv                                          AMP PEAK 22(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  10
  BLACK OR AFRICAN AMERICAN                                               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                  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"
D22V11, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.21) MUTATED    3 57
  AMP PEAK 22(20Q11.21) WILD-TYPE  8 70
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED      3   57
  AMP PEAK 22(20Q11.21) WILD-TYPE    8   70
                        clus
vv                       AMP PEAK 22(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            57
                        clus
vv                       AMP PEAK 22(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                              70
[1] 2 2
[1] FALSE
D22V12, continuous
D22V13, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.21) MUTATED   18  8
  AMP PEAK 22(20Q11.21) WILD-TYPE 30 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED     18    8
  AMP PEAK 22(20Q11.21) WILD-TYPE   30   11
            clus
vv           AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  TUMOR FREE                            18                              30
  WITH TUMOR                             8                              11
[1] 2 2
[1] FALSE
                                 vv
clus                              NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 22(20Q11.21) MUTATED         1      6       1            63       5
  AMP PEAK 22(20Q11.21) WILD-TYPE       0      4       5            84       7
D22V14, multiclass
               clus
vv              AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  NIGERIA                                   1                               0
  RUSSIA                                    6                               4
  UKRAINE                                   1                               5
  UNITED STATES                            63                              84
  VIETNAM                                   5                               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  AMP PEAK 22(20Q11.21) MUTATED    4 32 35  1  4
  AMP PEAK 22(20Q11.21) WILD-TYPE 10 51 37  0  1
D22V15, multiclass
    clus
vv   AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  G1                             4                              10
  G2                            32                              51
  G3                            35                              37
  G4                             1                               0
  GX                             4                               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V16, continuous
D22V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 22(20Q11.21) MUTATED                                            11
  AMP PEAK 22(20Q11.21) WILD-TYPE                                          10
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 22(20Q11.21) MUTATED                                        5
  AMP PEAK 22(20Q11.21) WILD-TYPE                                      3
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 22(20Q11.21) MUTATED                                                 0
  AMP PEAK 22(20Q11.21) WILD-TYPE                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 22(20Q11.21) MUTATED               13                  32
  AMP PEAK 22(20Q11.21) WILD-TYPE             23                  51
D22V18, multiclass
                                                 clus
vv                                                AMP PEAK 22(20Q11.21) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             13
  LIFELONG NON-SMOKER                                                        32
                                                 clus
vv                                                AMP PEAK 22(20Q11.21) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               23
  LIFELONG NON-SMOKER                                                          51
[1] 5 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
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 22(20Q11.21) MUTATED             7       13             6        3
  AMP PEAK 22(20Q11.21) WILD-TYPE          10       24             5        2
D22V20, multiclass
               clus
vv              AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  COMBINATION                               7                              10
  EXTERNAL                                 13                              24
  EXTERNAL BEAM                             6                               5
  INTERNAL                                  3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V21, binary
                                 cls
clus                              0 1
  AMP PEAK 22(20Q11.21) MUTATED   6 1
  AMP PEAK 22(20Q11.21) WILD-TYPE 5 2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED      6    1
  AMP PEAK 22(20Q11.21) WILD-TYPE    5    2
     clus
vv    AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  CGY                             6                               5
  GY                              1                               2
[1] 2 2
[1] FALSE
D22V22, continuous
D22V23, continuous
D22V24, continuous
D22V25, continuous
D22V26, continuous
D22V27, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 22(20Q11.21) MUTATED                                     0
  AMP PEAK 22(20Q11.21) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 22(20Q11.21) MUTATED                                     1
  AMP PEAK 22(20Q11.21) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  AMP PEAK 22(20Q11.21) MUTATED                         2
  AMP PEAK 22(20Q11.21) WILD-TYPE                       7
                                 vv
clus                              POSITIVE BLADDER MARGIN
  AMP PEAK 22(20Q11.21) MUTATED                         0
  AMP PEAK 22(20Q11.21) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  AMP PEAK 22(20Q11.21) MUTATED                         3
  AMP PEAK 22(20Q11.21) WILD-TYPE                       2
D22V28, multiclass
                                     clus
vv                                    AMP PEAK 22(20Q11.21) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         2
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         3
                                     clus
vv                                    AMP PEAK 22(20Q11.21) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                           7
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           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)
  AMP PEAK 22(20Q11.21) MUTATED                                               0
  AMP PEAK 22(20Q11.21) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 22(20Q11.21) MUTATED                                                4
  AMP PEAK 22(20Q11.21) WILD-TYPE                                              6
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 22(20Q11.21) MUTATED                                                                                  25
  AMP PEAK 22(20Q11.21) WILD-TYPE                                                                                29
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 22(20Q11.21) MUTATED                                                                                             32
  AMP PEAK 22(20Q11.21) WILD-TYPE                                                                                           45
D22V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 22(20Q11.21) 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)                                       25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            32
                                                                                              clus
vv                                                                                             AMP PEAK 22(20Q11.21) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                             6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V30, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.21) MUTATED   20 27
  AMP PEAK 22(20Q11.21) WILD-TYPE 34 32
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED     20   27
  AMP PEAK 22(20Q11.21) WILD-TYPE   34   32
         clus
vv        AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  ABSENT                             20                              34
  PRESENT                            27                              32
[1] 2 2
[1] FALSE
D22V31, continuous
D22V32, continuous
D22V33, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.21) MUTATED   11 33
  AMP PEAK 22(20Q11.21) WILD-TYPE 24 48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED     11   33
  AMP PEAK 22(20Q11.21) WILD-TYPE   24   48
                                          clus
vv                                         AMP PEAK 22(20Q11.21) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            33
                                          clus
vv                                         AMP PEAK 22(20Q11.21) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              48
[1] 2 2
[1] FALSE
D22V34, continuous
                                 vv
clus                              OTHER RADICAL HYSTERECTOMY
  AMP PEAK 22(20Q11.21) MUTATED       0                   48
  AMP PEAK 22(20Q11.21) WILD-TYPE     3                   65
                                 vv
clus                              SIMPLE HYSTERECTOMY
  AMP PEAK 22(20Q11.21) MUTATED                     2
  AMP PEAK 22(20Q11.21) WILD-TYPE                   3
D22V35, multiclass
                      clus
vv                     AMP PEAK 22(20Q11.21) MUTATED
  OTHER                                            0
  RADICAL HYSTERECTOMY                            48
  SIMPLE HYSTERECTOMY                              2
                      clus
vv                     AMP PEAK 22(20Q11.21) WILD-TYPE
  OTHER                                              3
  RADICAL HYSTERECTOMY                              65
  SIMPLE HYSTERECTOMY                                3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  AMP PEAK 22(20Q11.21) MUTATED              4          18         13
  AMP PEAK 22(20Q11.21) WILD-TYPE            4          22         27
D22V36, multiclass
              clus
vv             AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  CURRENT USER                             4                               4
  FORMER USER                             18                              22
  NEVER USED                              13                              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V37, continuous
D22V38, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.21) MUTATED   27  7
  AMP PEAK 22(20Q11.21) WILD-TYPE 46  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED     27    7
  AMP PEAK 22(20Q11.21) WILD-TYPE   46    7
         clus
vv        AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  ABSENT                             27                              46
  PRESENT                             7                               7
[1] 2 2
[1] FALSE
D22V39, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  AMP PEAK 22(20Q11.21) MUTATED     0    1   9   23    7  0   3    4    0   4
  AMP PEAK 22(20Q11.21) WILD-TYPE   2    0  13   28   14  3   3    2    8   9
                                 vv
clus                              T3B T4 TX
  AMP PEAK 22(20Q11.21) MUTATED     2  0  5
  AMP PEAK 22(20Q11.21) WILD-TYPE   0  1  2
D22V40, multiclass
      clus
vv     AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  T1A                              0                               2
  T1A1                             1                               0
  T1B                              9                              13
  T1B1                            23                              28
  T1B2                             7                              14
  T2                               0                               3
  T2A                              3                               3
  T2A1                             4                               2
  T2A2                             0                               8
  T2B                              4                               9
  T3B                              2                               0
  T4                               0                               1
  TX                               5                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V41, continuous

Clustering(23) Variable = AMP PEAK 23(XQ28) MUTATION ANALYSIS
D23V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 23(XQ28) MUTATED   38  3
  AMP PEAK 23(XQ28) WILD-TYPE 99 29
  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE 
                         41                         128 
  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE 
                          3                          29 
$`AMP PEAK 23(XQ28) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MP 
       57.04       144.16       177.04        46.32        53.16         3.58 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UH TCGA-DS-A3LQ 
       73.45        83.05        25.35       101.82        60.69        22.98 
TCGA-DS-A7WF TCGA-EA-A3HQ TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A556 TCGA-EA-A5O9 
       16.18         1.74        13.05         1.18        14.89        13.91 
TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RD 
       14.96        45.96         6.64         0.53         0.07         0.03 
TCGA-EK-A2RE TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-FU-A23L 
        0.36         0.07         0.10         0.10         0.03        23.84 
TCGA-FU-A3NI TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LL TCGA-MY-A5BD 
        1.45       137.16        66.81        78.71        36.36        29.72 
TCGA-MY-A5BF TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-R2-A69V 
        4.34         5.85         3.72         4.80        19.59 

$`AMP PEAK 23(XQ28) 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-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-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       30.21        35.01        57.73        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ 
        2.43        40.93        44.22        73.18        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43         0.82        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      182.93       134.33        15.48         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       85.55        94.95         9.34        13.61         2.73        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99       118.65        16.83 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
        7.33         8.28         0.76        12.36         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        0.62        14.50         1.35         1.35        14.50         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         0.69        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2R7 TCGA-EK-A2RC TCGA-EK-A2RJ 
       13.58        13.48        12.59         0.59         4.04         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
       23.70         2.24         0.10        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         4.47         6.12         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF 
       20.78        14.93         4.11       147.39       117.40        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       81.96        26.56        14.43        16.64        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-PN-A8MA 
        0.82        13.87         0.03         5.42         0.07         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73R TCGA-RA-A741 
        3.72         3.45         3.39         5.75         6.25         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE 
                       0.03                        0.03 
  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE 
                     177.04                      182.93 
  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE 
                      14.96                       12.74 
[1] "0.0 - 177.0 (15.0)" "0.0 - 182.9 (12.7)"
[1] "hr=" "3.9"
D23V2, continuous
                             vv
clus                          T1 T2+T3+T4
  AMP PEAK 23(XQ28) MUTATED   23        9
  AMP PEAK 23(XQ28) WILD-TYPE 74       30
D23V3, multiclass
          clus
vv         AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  T1                              23                          74
  T2+T3+T4                         9                          30
[1] 2 2
[1] FALSE
D23V4, binary
                             cls
clus                           0  1
  AMP PEAK 23(XQ28) MUTATED   24  7
  AMP PEAK 23(XQ28) WILD-TYPE 63 33
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 23(XQ28) MUTATED     24    7
  AMP PEAK 23(XQ28) WILD-TYPE   63   33
   clus
vv  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  0                        24                          63
  1                         7                          33
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK 23(XQ28) MUTATED   15  0 17
  AMP PEAK 23(XQ28) WILD-TYPE 57  3 48
D23V5, multiclass
    clus
vv   AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  M0                        15                          57
  M1                         0                           3
  MX                        17                          48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(XQ28) MUTATED               1                               36
  AMP PEAK 23(XQ28) WILD-TYPE             1                              108
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  AMP PEAK 23(XQ28) MUTATED                                               0
  AMP PEAK 23(XQ28) WILD-TYPE                                             4
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  AMP PEAK 23(XQ28) MUTATED                                     3
  AMP PEAK 23(XQ28) WILD-TYPE                                  17
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  AMP PEAK 23(XQ28) MUTATED                                           2
  AMP PEAK 23(XQ28) WILD-TYPE                                         0
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  AMP PEAK 23(XQ28) MUTATED                                              1
  AMP PEAK 23(XQ28) WILD-TYPE                                            3
D23V6, multiclass
                                               clus
vv                                              AMP PEAK 23(XQ28) MUTATED
  ADENOSQUAMOUS                                                         1
  CERVICAL SQUAMOUS CELL CARCINOMA                                     36
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          1
                                               clus
vv                                              AMP PEAK 23(XQ28) WILD-TYPE
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                      108
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                             cls
clus                            0   1
  AMP PEAK 23(XQ28) MUTATED     4  39
  AMP PEAK 23(XQ28) WILD-TYPE  23 110
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 23(XQ28) MUTATED      4   39
  AMP PEAK 23(XQ28) WILD-TYPE   23  110
     clus
vv    AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  NO                          4                          23
  YES                        39                         110
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(XQ28) MUTATED                                  2     2
  AMP PEAK 23(XQ28) WILD-TYPE                                5    13
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(XQ28) MUTATED                           5
  AMP PEAK 23(XQ28) WILD-TYPE                        13
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 23(XQ28) MUTATED                                           1    31
  AMP PEAK 23(XQ28) WILD-TYPE                                         0    99
D23V10, multiclass
                                           clus
vv                                          AMP PEAK 23(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             2
  BLACK OR AFRICAN AMERICAN                                         5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            31
                                           clus
vv                                          AMP PEAK 23(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    5
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              99
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                             cls
clus                           0  1
  AMP PEAK 23(XQ28) MUTATED    3 28
  AMP PEAK 23(XQ28) WILD-TYPE  8 99
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 23(XQ28) MUTATED      3   28
  AMP PEAK 23(XQ28) WILD-TYPE    8   99
                        clus
vv                       AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             3                           8
  NOT HISPANIC OR LATINO                        28                          99
[1] 2 2
[1] FALSE
D23V12, continuous
D23V13, binary
                             cls
clus                           0  1
  AMP PEAK 23(XQ28) MUTATED   15  2
  AMP PEAK 23(XQ28) WILD-TYPE 33 17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 23(XQ28) MUTATED     15    2
  AMP PEAK 23(XQ28) WILD-TYPE   33   17
            clus
vv           AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  TUMOR FREE                        15                          33
  WITH TUMOR                         2                          17
[1] 2 2
[1] FALSE
                             vv
clus                          NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  AMP PEAK 23(XQ28) MUTATED         0      3       1            38       1
  AMP PEAK 23(XQ28) WILD-TYPE       1      7       5           109      11
D23V14, multiclass
               clus
vv              AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  NIGERIA                               0                           1
  RUSSIA                                3                           7
  UKRAINE                               1                           5
  UNITED STATES                        38                         109
  VIETNAM                               1                          11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  AMP PEAK 23(XQ28) MUTATED    4 17 20  1  0
  AMP PEAK 23(XQ28) WILD-TYPE 10 66 52  0  5
D23V15, multiclass
    clus
vv   AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  G1                         4                          10
  G2                        17                          66
  G3                        20                          52
  G4                         1                           0
  GX                         0                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V16, continuous
D23V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  AMP PEAK 23(XQ28) MUTATED                                             3
  AMP PEAK 23(XQ28) WILD-TYPE                                          18
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  AMP PEAK 23(XQ28) MUTATED                                        2
  AMP PEAK 23(XQ28) WILD-TYPE                                      6
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  AMP PEAK 23(XQ28) MUTATED                                                 0
  AMP PEAK 23(XQ28) WILD-TYPE                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  AMP PEAK 23(XQ28) MUTATED                9                  18
  AMP PEAK 23(XQ28) WILD-TYPE             27                  65
D23V18, multiclass
                                                 clus
vv                                                AMP PEAK 23(XQ28) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         0
  CURRENT SMOKER                                                          9
  LIFELONG NON-SMOKER                                                    18
                                                 clus
vv                                                AMP PEAK 23(XQ28) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           27
  LIFELONG NON-SMOKER                                                      65
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V19, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  AMP PEAK 23(XQ28) MUTATED             3        9             1        1
  AMP PEAK 23(XQ28) WILD-TYPE          14       28            10        4
D23V20, multiclass
               clus
vv              AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  COMBINATION                           3                          14
  EXTERNAL                              9                          28
  EXTERNAL BEAM                         1                          10
  INTERNAL                              1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V21, binary
                             cls
clus                          0 1
  AMP PEAK 23(XQ28) MUTATED   3 1
  AMP PEAK 23(XQ28) WILD-TYPE 8 2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 23(XQ28) MUTATED      3    1
  AMP PEAK 23(XQ28) WILD-TYPE    8    2
     clus
vv    AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  CGY                         3                           8
  GY                          1                           2
[1] 2 2
[1] FALSE
D23V22, continuous
D23V23, continuous
D23V24, continuous
D23V25, continuous
D23V26, continuous
D23V27, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 23(XQ28) MUTATED                                     1
  AMP PEAK 23(XQ28) WILD-TYPE                                   1
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  AMP PEAK 23(XQ28) MUTATED                                     0
  AMP PEAK 23(XQ28) WILD-TYPE                                   6
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  AMP PEAK 23(XQ28) MUTATED                         1                       0
  AMP PEAK 23(XQ28) WILD-TYPE                       8                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  AMP PEAK 23(XQ28) MUTATED                         2
  AMP PEAK 23(XQ28) WILD-TYPE                       3
D23V28, multiclass
                                     clus
vv                                    AMP PEAK 23(XQ28) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  OTHER LOCATION, SPECIFY                                     1
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     2
                                     clus
vv                                    AMP PEAK 23(XQ28) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           6
  OTHER LOCATION, SPECIFY                                       8
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       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)
  AMP PEAK 23(XQ28) MUTATED                                               0
  AMP PEAK 23(XQ28) WILD-TYPE                                             2
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  AMP PEAK 23(XQ28) MUTATED                                                2
  AMP PEAK 23(XQ28) WILD-TYPE                                              8
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  AMP PEAK 23(XQ28) MUTATED                                                                                  14
  AMP PEAK 23(XQ28) WILD-TYPE                                                                                40
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  AMP PEAK 23(XQ28) MUTATED                                                                                             18
  AMP PEAK 23(XQ28) WILD-TYPE                                                                                           59
D23V29, multiclass
                                                                                              clus
vv                                                                                             AMP PEAK 23(XQ28) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        18
                                                                                              clus
vv                                                                                             AMP PEAK 23(XQ28) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          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"
D23V30, binary
                             cls
clus                           0  1
  AMP PEAK 23(XQ28) MUTATED   16 14
  AMP PEAK 23(XQ28) WILD-TYPE 38 45
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 23(XQ28) MUTATED     16   14
  AMP PEAK 23(XQ28) WILD-TYPE   38   45
         clus
vv        AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  ABSENT                         16                          38
  PRESENT                        14                          45
[1] 2 2
[1] FALSE
D23V31, continuous
D23V32, continuous
D23V33, binary
                             cls
clus                           0  1
  AMP PEAK 23(XQ28) MUTATED   10 17
  AMP PEAK 23(XQ28) WILD-TYPE 25 64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 23(XQ28) MUTATED     10   17
  AMP PEAK 23(XQ28) WILD-TYPE   25   64
                                          clus
vv                                         AMP PEAK 23(XQ28) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        17
                                          clus
vv                                         AMP PEAK 23(XQ28) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          64
[1] 2 2
[1] FALSE
D23V34, continuous
                             vv
clus                          OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  AMP PEAK 23(XQ28) MUTATED       2                   27                   1
  AMP PEAK 23(XQ28) WILD-TYPE     1                   86                   4
D23V35, multiclass
                      clus
vv                     AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  OTHER                                        2                           1
  RADICAL HYSTERECTOMY                        27                          86
  SIMPLE HYSTERECTOMY                          1                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  AMP PEAK 23(XQ28) MUTATED              2           9          9
  AMP PEAK 23(XQ28) WILD-TYPE            6          31         31
D23V36, multiclass
              clus
vv             AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  CURRENT USER                         2                           6
  FORMER USER                          9                          31
  NEVER USED                           9                          31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V37, continuous
D23V38, binary
                             cls
clus                           0  1
  AMP PEAK 23(XQ28) MUTATED   21  2
  AMP PEAK 23(XQ28) WILD-TYPE 52 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 23(XQ28) MUTATED     21    2
  AMP PEAK 23(XQ28) WILD-TYPE   52   12
         clus
vv        AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  ABSENT                         21                          52
  PRESENT                         2                          12
[1] 2 2
[1] FALSE
D23V39, continuous
[1] "Remove cluster labels:"    "AMP PEAK 23(XQ28) MUTATED"
clus
  AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE 
                          2                           7 
                 TCGA-C5-A1BN                  TCGA-C5-A1MH 
"AMP PEAK 23(XQ28) WILD-TYPE" "AMP PEAK 23(XQ28) WILD-TYPE" 
                 TCGA-C5-A1MN                  TCGA-HM-A3JK 
"AMP PEAK 23(XQ28) WILD-TYPE" "AMP PEAK 23(XQ28) WILD-TYPE" 
                 TCGA-JW-A852                  TCGA-MU-A51Y 
"AMP PEAK 23(XQ28) WILD-TYPE" "AMP PEAK 23(XQ28) WILD-TYPE" 
                 TCGA-MU-A8JM 
"AMP PEAK 23(XQ28) WILD-TYPE" 
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  AMP PEAK 23(XQ28) MUTATED     0    0   6   13    4  1   2    2    2   1   1
  AMP PEAK 23(XQ28) WILD-TYPE   2    1  16   38   17  2   4    4    6  12   1
                             vv
clus                          T4 TX
  AMP PEAK 23(XQ28) MUTATED    0  2
  AMP PEAK 23(XQ28) WILD-TYPE  1  5
D23V40, multiclass
      clus
vv     AMP PEAK 23(XQ28) MUTATED AMP PEAK 23(XQ28) WILD-TYPE
  T1A                          0                           2
  T1A1                         0                           1
  T1B                          6                          16
  T1B1                        13                          38
  T1B2                         4                          17
  T2                           1                           2
  T2A                          2                           4
  T2A1                         2                           4
  T2A2                         2                           6
  T2B                          1                          12
  T3B                          1                           1
  T4                           0                           1
  TX                           2                           5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V41, continuous

Clustering(24) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    19   4
  DEL PEAK  1(1P36.31) WILD-TYPE 118  28
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            23                            146 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             4                             28 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BL TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ 
       11.44       173.29        57.73        53.16        35.61         0.46 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CM TCGA-C5-A7UH TCGA-C5-A7X3 
       73.18        83.05        52.01         9.67        60.69         9.34 
TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A556 TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EK-A2RM 
        1.32        14.50        14.89         0.53         1.18         2.24 
TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A3EO TCGA-IR-A3LF TCGA-Q1-A6DT 
       14.70         4.47         2.17        96.95         3.39 

$`DEL PEAK  1(1P36.31) 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-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-A1M9 TCGA-C5-A1MH TCGA-C5-A1MK 
       31.40        46.32        30.21        35.01        38.99         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ 
       40.93         3.58        44.22        73.45        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43         0.82        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC 
       25.35       101.82       134.33        15.48        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       85.55        94.95        13.61         2.73        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18         7.33         8.28         0.76        12.36         1.74 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35         1.81        12.66        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91         0.69        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       12.59        45.96         6.64         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-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-A69M 
        0.10         0.03        20.35         7.92         6.94         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84         0.92         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
        4.11       147.39       137.16        66.81       117.40        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.46                           0.03 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        173.29                         182.93 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         14.50                          13.53 
[1] "0.5 - 173.3 (14.5)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.2"
D24V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK  1(1P36.31) MUTATED   12        4
  DEL PEAK  1(1P36.31) WILD-TYPE 85       35
D24V3, multiclass
          clus
vv         DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                                 12                             85
  T2+T3+T4                            4                             35
[1] 2 2
[1] FALSE
D24V4, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   11  4
  DEL PEAK  1(1P36.31) WILD-TYPE 76 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     11    4
  DEL PEAK  1(1P36.31) WILD-TYPE   76   36
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                           11                             76
  1                            4                             36
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK  1(1P36.31) MUTATED    9  1  7
  DEL PEAK  1(1P36.31) WILD-TYPE 63  2 58
D24V5, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  M0                            9                             63
  M1                            1                              2
  MX                            7                             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.31) MUTATED               0                               17
  DEL PEAK  1(1P36.31) WILD-TYPE             2                              127
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  1(1P36.31) MUTATED                                               2
  DEL PEAK  1(1P36.31) WILD-TYPE                                             2
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  1(1P36.31) MUTATED                                     5
  DEL PEAK  1(1P36.31) WILD-TYPE                                  15
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  1(1P36.31) MUTATED                                           1
  DEL PEAK  1(1P36.31) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  1(1P36.31) MUTATED                                              0
  DEL PEAK  1(1P36.31) WILD-TYPE                                            4
D24V6, multiclass
                                               clus
vv                                              DEL PEAK  1(1P36.31) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        17
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              DEL PEAK  1(1P36.31) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         127
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       15
  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"
D24V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     6  19
  DEL PEAK  1(1P36.31) WILD-TYPE  21 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      6   19
  DEL PEAK  1(1P36.31) WILD-TYPE   21  130
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                             6                             21
  YES                           19                            130
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.31) MUTATED                                  0     2
  DEL PEAK  1(1P36.31) WILD-TYPE                                7    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.31) MUTATED                           2
  DEL PEAK  1(1P36.31) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  1(1P36.31) MUTATED                                           0
  DEL PEAK  1(1P36.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK  1(1P36.31) MUTATED      21
  DEL PEAK  1(1P36.31) WILD-TYPE   109
D24V10, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               21
                                           clus
vv                                          DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D24V11, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     2  19
  DEL PEAK  1(1P36.31) WILD-TYPE   9 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      2   19
  DEL PEAK  1(1P36.31) WILD-TYPE    9  108
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            108
[1] 2 2
[1] FALSE
D24V12, continuous
D24V13, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   10  2
  DEL PEAK  1(1P36.31) WILD-TYPE 38 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     10    2
  DEL PEAK  1(1P36.31) WILD-TYPE   38   17
            clus
vv           DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  TUMOR FREE                           10                             38
  WITH TUMOR                            2                             17
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  1(1P36.31) MUTATED         0      2       0            22       1
  DEL PEAK  1(1P36.31) WILD-TYPE       1      8       6           125      11
D24V14, multiclass
               clus
vv              DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  0                              6
  UNITED STATES                           22                            125
  VIETNAM                                  1                             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK  1(1P36.31) MUTATED    2 13  9  0  1
  DEL PEAK  1(1P36.31) WILD-TYPE 12 70 63  1  4
D24V15, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  G1                            2                             12
  G2                           13                             70
  G3                            9                             63
  G4                            0                              1
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V16, continuous
D24V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  1(1P36.31) MUTATED                                             5
  DEL PEAK  1(1P36.31) WILD-TYPE                                          16
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  1(1P36.31) MUTATED                                        0
  DEL PEAK  1(1P36.31) WILD-TYPE                                      8
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  1(1P36.31) MUTATED                                                 0
  DEL PEAK  1(1P36.31) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  1(1P36.31) MUTATED                5                  10
  DEL PEAK  1(1P36.31) WILD-TYPE             31                  73
D24V18, multiclass
                                                 clus
vv                                                DEL PEAK  1(1P36.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             5
  LIFELONG NON-SMOKER                                                       10
                                                 clus
vv                                                DEL PEAK  1(1P36.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              31
  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"
D24V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  1(1P36.31) MUTATED             4        4             2        1
  DEL PEAK  1(1P36.31) WILD-TYPE          13       33             9        4
D24V20, multiclass
               clus
vv              DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  COMBINATION                              4                             13
  EXTERNAL                                 4                             33
  EXTERNAL BEAM                            2                              9
  INTERNAL                                 1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V21, binary
                                cls
clus                             0 1
  DEL PEAK  1(1P36.31) MUTATED   3 0
  DEL PEAK  1(1P36.31) WILD-TYPE 8 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      3    0
  DEL PEAK  1(1P36.31) WILD-TYPE    8    3
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CGY                            3                              8
  GY                             0                              3
[1] 2 2
[1] FALSE
D24V22, continuous
D24V23, continuous
D24V24, continuous
D24V25, continuous
D24V26, continuous
D24V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  1(1P36.31) MUTATED                                     1
  DEL PEAK  1(1P36.31) WILD-TYPE                                   1
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  1(1P36.31) MUTATED                                     1
  DEL PEAK  1(1P36.31) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK  1(1P36.31) MUTATED                         0
  DEL PEAK  1(1P36.31) WILD-TYPE                       9
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK  1(1P36.31) MUTATED                         0
  DEL PEAK  1(1P36.31) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK  1(1P36.31) MUTATED                         2
  DEL PEAK  1(1P36.31) WILD-TYPE                       3
D24V28, multiclass
                                     clus
vv                                    DEL PEAK  1(1P36.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        0
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK  1(1P36.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          9
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK  1(1P36.31) MUTATED                                               0
  DEL PEAK  1(1P36.31) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  1(1P36.31) MUTATED                                                1
  DEL PEAK  1(1P36.31) WILD-TYPE                                              9
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  1(1P36.31) MUTATED                                                                                   8
  DEL PEAK  1(1P36.31) WILD-TYPE                                                                                46
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  1(1P36.31) MUTATED                                                                                              9
  DEL PEAK  1(1P36.31) WILD-TYPE                                                                                           68
D24V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  1(1P36.31) 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)                                       8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            9
                                                                                              clus
vv                                                                                             DEL PEAK  1(1P36.31) 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)                                        46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V30, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    8  8
  DEL PEAK  1(1P36.31) WILD-TYPE 46 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      8    8
  DEL PEAK  1(1P36.31) WILD-TYPE   46   51
         clus
vv        DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  ABSENT                             8                             46
  PRESENT                            8                             51
[1] 2 2
[1] FALSE
D24V31, continuous
D24V32, continuous
D24V33, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    4  7
  DEL PEAK  1(1P36.31) WILD-TYPE 31 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      4    7
  DEL PEAK  1(1P36.31) WILD-TYPE   31   74
                                          clus
vv                                         DEL PEAK  1(1P36.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            7
                                          clus
vv                                         DEL PEAK  1(1P36.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             74
[1] 2 2
[1] FALSE
D24V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  1(1P36.31) MUTATED       1                   13                   1
  DEL PEAK  1(1P36.31) WILD-TYPE     2                  100                   4
D24V35, multiclass
                      clus
vv                     DEL PEAK  1(1P36.31) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           13
  SIMPLE HYSTERECTOMY                             1
                      clus
vv                     DEL PEAK  1(1P36.31) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                            100
  SIMPLE HYSTERECTOMY                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK  1(1P36.31) MUTATED              1           6          6
  DEL PEAK  1(1P36.31) WILD-TYPE            7          34         34
D24V36, multiclass
              clus
vv             DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CURRENT USER                            1                              7
  FORMER USER                             6                             34
  NEVER USED                              6                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V37, continuous
D24V38, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   14  1
  DEL PEAK  1(1P36.31) WILD-TYPE 59 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     14    1
  DEL PEAK  1(1P36.31) WILD-TYPE   59   13
         clus
vv        DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  ABSENT                            14                             59
  PRESENT                            1                             13
[1] 2 2
[1] FALSE
D24V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK  1(1P36.31) MUTATED     0    0   3    7    2  1   1    1    0   1
  DEL PEAK  1(1P36.31) WILD-TYPE   2    1  19   44   19  2   5    5    8  12
                                vv
clus                             T3B T4 TX
  DEL PEAK  1(1P36.31) MUTATED     0  0  1
  DEL PEAK  1(1P36.31) WILD-TYPE   2  1  6
D24V40, multiclass
      clus
vv     DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1A                             0                              2
  T1A1                            0                              1
  T1B                             3                             19
  T1B1                            7                             44
  T1B2                            2                             19
  T2                              1                              2
  T2A                             1                              5
  T2A1                            1                              5
  T2A2                            0                              8
  T2B                             1                             12
  T3B                             0                              2
  T4                              0                              1
  TX                              1                              6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V41, continuous

Clustering(25) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    12   4
  DEL PEAK  2(1P13.2) WILD-TYPE 125  28
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           16                           153 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            4                            28 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-C5-A1BF TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A7CH TCGA-C5-A7UH 
       18.74        35.61        73.18        78.35        25.35        60.69 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-DS-A0VN TCGA-EA-A3HR TCGA-EA-A3QE TCGA-EX-A69L 
       94.95        13.61       118.65         1.32         1.18         4.47 
TCGA-FU-A3NI TCGA-HG-A2PA TCGA-LP-A4AW TCGA-Q1-A6DT 
        1.45        25.41         0.89         3.39 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99         0.46         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        73.45        83.05       100.14        38.43         0.82 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       182.93       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        9.34         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        0.76        12.36         1.74         0.82         0.62        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         0.26        14.89         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        6.64         0.53         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.36         1.18        23.70         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-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-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.35         1.32         1.97         1.12        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       16.64        19.33        20.48        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.10         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        5.85         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.89                          0.03 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       118.65                        182.93 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       22.045                        13.050 
[1] "0.9 - 118.7 (22.0)" "0.0 - 182.9 (13.1)"
[1] "hr=" "1.1"
D25V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK  2(1P13.2) MUTATED   10        1
  DEL PEAK  2(1P13.2) WILD-TYPE 87       38
D25V3, multiclass
          clus
vv         DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                                10                            87
  T2+T3+T4                           1                            38
[1] 2 2
[1] FALSE
D25V4, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   10  2
  DEL PEAK  2(1P13.2) WILD-TYPE 77 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     10    2
  DEL PEAK  2(1P13.2) WILD-TYPE   77   38
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          10                            77
  1                           2                            38
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  2(1P13.2) MUTATED    9  0  4
  DEL PEAK  2(1P13.2) WILD-TYPE 63  3 61
D25V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  M0                           9                            63
  M1                           0                             3
  MX                           4                            61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.2) MUTATED               0                               18
  DEL PEAK  2(1P13.2) WILD-TYPE             2                              126
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  2(1P13.2) MUTATED                                               0
  DEL PEAK  2(1P13.2) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  2(1P13.2) MUTATED                                     1
  DEL PEAK  2(1P13.2) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  2(1P13.2) MUTATED                                           0
  DEL PEAK  2(1P13.2) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  2(1P13.2) MUTATED                                              0
  DEL PEAK  2(1P13.2) WILD-TYPE                                            4
D25V6, multiclass
                                               clus
vv                                              DEL PEAK  2(1P13.2) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       18
  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                                              DEL PEAK  2(1P13.2) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        126
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     5  14
  DEL PEAK  2(1P13.2) WILD-TYPE  22 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      5   14
  DEL PEAK  2(1P13.2) WILD-TYPE   22  135
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                            5                            22
  YES                          14                           135
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P13.2) MUTATED                                  0     2
  DEL PEAK  2(1P13.2) WILD-TYPE                                7    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P13.2) MUTATED                           2
  DEL PEAK  2(1P13.2) WILD-TYPE                        16
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           0    15
  DEL PEAK  2(1P13.2) WILD-TYPE                                         1   115
D25V10, multiclass
                                           clus
vv                                          DEL PEAK  2(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              15
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               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"
D25V11, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     1  15
  DEL PEAK  2(1P13.2) WILD-TYPE  10 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1   15
  DEL PEAK  2(1P13.2) WILD-TYPE   10  112
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           112
[1] 2 2
[1] FALSE
D25V12, continuous
D25V13, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    3  2
  DEL PEAK  2(1P13.2) WILD-TYPE 45 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      3    2
  DEL PEAK  2(1P13.2) WILD-TYPE   45   17
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  TUMOR FREE                           3                            45
  WITH TUMOR                           2                            17
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  2(1P13.2) MUTATED         0      2       0            16       1
  DEL PEAK  2(1P13.2) WILD-TYPE       1      8       6           131      11
D25V14, multiclass
               clus
vv              DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  2                             8
  UKRAINE                                 0                             6
  UNITED STATES                          16                           131
  VIETNAM                                 1                            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  2(1P13.2) MUTATED    2 10  5  0  1
  DEL PEAK  2(1P13.2) WILD-TYPE 12 73 67  1  4
D25V15, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  G1                           2                            12
  G2                          10                            73
  G3                           5                            67
  G4                           0                             1
  GX                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V16, continuous
D25V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  2(1P13.2) MUTATED                                             0
  DEL PEAK  2(1P13.2) WILD-TYPE                                          21
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  2(1P13.2) MUTATED                                        0
  DEL PEAK  2(1P13.2) WILD-TYPE                                      8
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  2(1P13.2) MUTATED                                                 0
  DEL PEAK  2(1P13.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  2(1P13.2) MUTATED                6                  10
  DEL PEAK  2(1P13.2) WILD-TYPE             30                  73
D25V18, multiclass
                                                 clus
vv                                                DEL PEAK  2(1P13.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                            6
  LIFELONG NON-SMOKER                                                      10
                                                 clus
vv                                                DEL PEAK  2(1P13.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             30
  LIFELONG NON-SMOKER                                                        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"
D25V19, continuous
[1] "Remove cluster labels:"      "DEL PEAK  2(1P13.2) MUTATED"
clus
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            2                            46 
                   TCGA-BI-A0VR                    TCGA-C5-A1BI 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1BJ                    TCGA-C5-A1BL 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1BN                    TCGA-C5-A1BQ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1M7                    TCGA-C5-A1ME 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1MF                    TCGA-C5-A2LS 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A2LV                    TCGA-C5-A2LX 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A2LZ                    TCGA-C5-A2M2 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A3HD                    TCGA-C5-A3HF 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A7CJ                    TCGA-C5-A7CL 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A7CO                    TCGA-C5-A7UE 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A7X8                    TCGA-DR-A0ZM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-DS-A5RQ                    TCGA-EA-A556 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A2QG 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FU-A3EO                    TCGA-FU-A3HY 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FU-A3TQ                    TCGA-FU-A3TX 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FU-A3WB                    TCGA-FU-A3YQ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FU-A5XV                    TCGA-FU-A770 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-HM-A4S6                    TCGA-HM-A6W2 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-IR-A3L7                    TCGA-IR-A3LB 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-IR-A3LH                    TCGA-JW-A5VI 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-JW-A5VK                    TCGA-MU-A5YI 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MU-A8JM                    TCGA-Q1-A6DW 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-RA-A741                    TCGA-UC-A7PD 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  2(1P13.2) MUTATED             3        1             2        1
  DEL PEAK  2(1P13.2) WILD-TYPE          14       36             9        4
D25V20, multiclass
               clus
vv              DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  COMBINATION                             3                            14
  EXTERNAL                                1                            36
  EXTERNAL BEAM                           2                             9
  INTERNAL                                1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V21, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    0  0
  DEL PEAK  2(1P13.2) WILD-TYPE 11  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      0    0
  DEL PEAK  2(1P13.2) WILD-TYPE   11    3
D25V22, continuous
D25V23, continuous
D25V24, continuous
D25V25, continuous
D25V26, continuous
D25V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  2(1P13.2) MUTATED                                     0
  DEL PEAK  2(1P13.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  2(1P13.2) MUTATED                                     0
  DEL PEAK  2(1P13.2) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  2(1P13.2) MUTATED                         1                       0
  DEL PEAK  2(1P13.2) WILD-TYPE                       8                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  2(1P13.2) MUTATED                         0
  DEL PEAK  2(1P13.2) WILD-TYPE                       5
D25V28, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  2(1P13.2) MUTATED"
clus
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            1                            22 
                   TCGA-BI-A20A                    TCGA-C5-A0TN 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A1BE                    TCGA-C5-A1BM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-C5-A2LX                    TCGA-DR-A0ZM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A3LQ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EA-A50E                    TCGA-EK-A2RN 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-EX-A1H5 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EX-A449                    TCGA-FU-A3EO 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-HM-A4S6                    TCGA-IR-A3LH 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-IR-A3LI                    TCGA-IR-A3LK 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-MU-A8JM                    TCGA-UC-A7PD 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                               vv
clus                            INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK  2(1P13.2) MUTATED                                               0
  DEL PEAK  2(1P13.2) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  2(1P13.2) MUTATED                                                2
  DEL PEAK  2(1P13.2) WILD-TYPE                                              8
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  2(1P13.2) MUTATED                                                                                   3
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                51
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  2(1P13.2) MUTATED                                                                                              7
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                           70
D25V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  2(1P13.2) 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)                           7
                                                                                              clus
vv                                                                                             DEL PEAK  2(1P13.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V30, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6  3
  DEL PEAK  2(1P13.2) WILD-TYPE 48 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6    3
  DEL PEAK  2(1P13.2) WILD-TYPE   48   56
         clus
vv        DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ABSENT                            6                            48
  PRESENT                           3                            56
[1] 2 2
[1] FALSE
D25V31, continuous
D25V32, continuous
D25V33, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    7  8
  DEL PEAK  2(1P13.2) WILD-TYPE 28 73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7    8
  DEL PEAK  2(1P13.2) WILD-TYPE   28   73
                                          clus
vv                                         DEL PEAK  2(1P13.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           8
                                          clus
vv                                         DEL PEAK  2(1P13.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            73
[1] 2 2
[1] FALSE
D25V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  2(1P13.2) MUTATED       0                    9                   0
  DEL PEAK  2(1P13.2) WILD-TYPE     3                  104                   5
D25V35, multiclass
                      clus
vv                     DEL PEAK  2(1P13.2) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                           9
  SIMPLE HYSTERECTOMY                            0
                      clus
vv                     DEL PEAK  2(1P13.2) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                           104
  SIMPLE HYSTERECTOMY                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  2(1P13.2) MUTATED              1           3          3
  DEL PEAK  2(1P13.2) WILD-TYPE            7          37         37
D25V36, multiclass
              clus
vv             DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CURRENT USER                           1                             7
  FORMER USER                            3                            37
  NEVER USED                             3                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V37, continuous
D25V38, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    7  1
  DEL PEAK  2(1P13.2) WILD-TYPE 66 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7    1
  DEL PEAK  2(1P13.2) WILD-TYPE   66   13
         clus
vv        DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ABSENT                            7                            66
  PRESENT                           1                            13
[1] 2 2
[1] FALSE
D25V39, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK  2(1P13.2) MUTATED     1    0   2    5    2  0   1    0    0   0   0
  DEL PEAK  2(1P13.2) WILD-TYPE   1    1  20   46   19  3   5    6    8  13   2
                               vv
clus                            T4 TX
  DEL PEAK  2(1P13.2) MUTATED    0  2
  DEL PEAK  2(1P13.2) WILD-TYPE  1  5
D25V40, multiclass
      clus
vv     DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1A                            1                             1
  T1A1                           0                             1
  T1B                            2                            20
  T1B1                           5                            46
  T1B2                           2                            19
  T2                             0                             3
  T2A                            1                             5
  T2A1                           0                             6
  T2A2                           0                             8
  T2B                            0                            13
  T3B                            0                             2
  T4                             0                             1
  TX                             2                             5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V41, continuous

Clustering(26) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    27   3
  DEL PEAK  3(2Q22.1) WILD-TYPE 110  29
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           30                           139 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            3                            29 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A2LV 
       36.56         5.46        30.21        38.99        73.18        73.45 
TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7UH TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WH 
       18.02       182.93        60.69       118.65        22.98         7.33 
TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2IP 
        1.32         1.35        12.66        14.99        14.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EX-A69L TCGA-HM-A3JJ TCGA-HM-A6W2 
        0.53         1.18         0.10         4.47        21.67         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-R2-A69V 
      147.39        78.71         4.34         3.72         3.45        19.59 

$`DEL PEAK  3(2Q22.1) 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-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-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       31.40        46.32        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX 
        0.46         2.43        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-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        25.35       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       73.41        17.19        85.55        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
        2.73        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18         8.28         0.76        12.36         1.74 
TCGA-EA-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-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-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       13.91         0.69        13.58        13.48        12.59        45.96 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        0.59         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-A69M TCGA-FU-A23K TCGA-FU-A23L 
        7.92         6.94        14.70         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.12        25.41        20.78        14.93       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        81.96        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       16.64        19.33        20.48        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.10         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        5.42        29.72         0.07         2.96         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD 
        3.72         5.75         4.80         6.25         3.88        11.67 
TCGA-UC-A7PF 
       93.99 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       182.93                        177.04 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       14.975                        13.480 
[1] "0.1 - 182.9 (15.0)" "0.0 - 177.0 (13.5)"
[1] "hr=" "2.5"
D26V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK  3(2Q22.1) MUTATED   18        7
  DEL PEAK  3(2Q22.1) WILD-TYPE 79       32
D26V3, multiclass
          clus
vv         DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                                18                            79
  T2+T3+T4                           7                            32
[1] 2 2
[1] FALSE
D26V4, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   18  6
  DEL PEAK  3(2Q22.1) WILD-TYPE 69 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     18    6
  DEL PEAK  3(2Q22.1) WILD-TYPE   69   34
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          18                            69
  1                           6                            34
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  3(2Q22.1) MUTATED   14  1 11
  DEL PEAK  3(2Q22.1) WILD-TYPE 58  2 54
D26V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  M0                          14                            58
  M1                           1                             2
  MX                          11                            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED               1                               27
  DEL PEAK  3(2Q22.1) WILD-TYPE             1                              117
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  3(2Q22.1) MUTATED                                               0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                     1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  3(2Q22.1) MUTATED                                           0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  3(2Q22.1) MUTATED                                              1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                            3
D26V6, multiclass
                                               clus
vv                                              DEL PEAK  3(2Q22.1) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       27
  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                                              DEL PEAK  3(2Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        117
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     8  22
  DEL PEAK  3(2Q22.1) WILD-TYPE  19 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      8   22
  DEL PEAK  3(2Q22.1) WILD-TYPE   19  127
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                            8                            19
  YES                          22                           127
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q22.1) MUTATED                                  0     3
  DEL PEAK  3(2Q22.1) WILD-TYPE                                7    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(2Q22.1) MUTATED                           5
  DEL PEAK  3(2Q22.1) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(2Q22.1) MUTATED                                           0    21
  DEL PEAK  3(2Q22.1) WILD-TYPE                                         1   109
D26V10, multiclass
                                           clus
vv                                          DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              21
                                           clus
vv                                          DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               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"
D26V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     0  24
  DEL PEAK  3(2Q22.1) WILD-TYPE  11 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      0   24
  DEL PEAK  3(2Q22.1) WILD-TYPE   11  103
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          24
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           103
[1] 2 2
[1] FALSE
D26V12, continuous
D26V13, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED    7  4
  DEL PEAK  3(2Q22.1) WILD-TYPE 41 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      7    4
  DEL PEAK  3(2Q22.1) WILD-TYPE   41   15
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  TUMOR FREE                           7                            41
  WITH TUMOR                           4                            15
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  3(2Q22.1) MUTATED         0      2       1            25       2
  DEL PEAK  3(2Q22.1) WILD-TYPE       1      8       5           122      10
D26V14, multiclass
               clus
vv              DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  2                             8
  UKRAINE                                 1                             5
  UNITED STATES                          25                           122
  VIETNAM                                 2                            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  3(2Q22.1) MUTATED    1 11 17  1  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 13 72 55  0  5
D26V15, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  G1                           1                            13
  G2                          11                            72
  G3                          17                            55
  G4                           1                             0
  GX                           0                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V16, continuous
D26V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  3(2Q22.1) MUTATED                                             2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                          19
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  3(2Q22.1) MUTATED                                        2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  3(2Q22.1) MUTATED                                                 0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  3(2Q22.1) MUTATED                5                  16
  DEL PEAK  3(2Q22.1) WILD-TYPE             31                  67
D26V18, multiclass
                                                 clus
vv                                                DEL PEAK  3(2Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                            5
  LIFELONG NON-SMOKER                                                      16
                                                 clus
vv                                                DEL PEAK  3(2Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             31
  LIFELONG NON-SMOKER                                                        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"
D26V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  3(2Q22.1) MUTATED             3        8             5        1
  DEL PEAK  3(2Q22.1) WILD-TYPE          14       29             6        4
D26V20, multiclass
               clus
vv              DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  COMBINATION                             3                            14
  EXTERNAL                                8                            29
  EXTERNAL BEAM                           5                             6
  INTERNAL                                1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V21, binary
                               cls
clus                            0 1
  DEL PEAK  3(2Q22.1) MUTATED   2 1
  DEL PEAK  3(2Q22.1) WILD-TYPE 9 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      2    1
  DEL PEAK  3(2Q22.1) WILD-TYPE    9    2
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  CGY                           2                             9
  GY                            1                             2
[1] 2 2
[1] FALSE
D26V22, continuous
D26V23, continuous
D26V24, continuous
D26V25, continuous
D26V26, continuous
D26V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  3(2Q22.1) MUTATED                                     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  3(2Q22.1) MUTATED                                     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  3(2Q22.1) MUTATED                         3                       0
  DEL PEAK  3(2Q22.1) WILD-TYPE                       6                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  3(2Q22.1) MUTATED                         1
  DEL PEAK  3(2Q22.1) WILD-TYPE                       4
D26V28, multiclass
                                     clus
vv                                    DEL PEAK  3(2Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       3
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  3(2Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                         6
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK  3(2Q22.1) MUTATED                                               1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  3(2Q22.1) MUTATED                                                3
  DEL PEAK  3(2Q22.1) WILD-TYPE                                              7
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  3(2Q22.1) MUTATED                                                                                   7
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                                47
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  3(2Q22.1) MUTATED                                                                                             14
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                                           63
D26V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  3(2Q22.1) 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)                                      7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          14
                                                                                              clus
vv                                                                                             DEL PEAK  3(2Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       47
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V30, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   10 10
  DEL PEAK  3(2Q22.1) WILD-TYPE 44 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     10   10
  DEL PEAK  3(2Q22.1) WILD-TYPE   44   49
         clus
vv        DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  ABSENT                           10                            44
  PRESENT                          10                            49
[1] 2 2
[1] FALSE
D26V31, continuous
D26V32, continuous
D26V33, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED    5 16
  DEL PEAK  3(2Q22.1) WILD-TYPE 30 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      5   16
  DEL PEAK  3(2Q22.1) WILD-TYPE   30   65
                                          clus
vv                                         DEL PEAK  3(2Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          16
                                          clus
vv                                         DEL PEAK  3(2Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            65
[1] 2 2
[1] FALSE
D26V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  3(2Q22.1) MUTATED       1                   22                   0
  DEL PEAK  3(2Q22.1) WILD-TYPE     2                   91                   5
D26V35, multiclass
                      clus
vv                     DEL PEAK  3(2Q22.1) MUTATED
  OTHER                                          1
  RADICAL HYSTERECTOMY                          22
  SIMPLE HYSTERECTOMY                            0
                      clus
vv                     DEL PEAK  3(2Q22.1) WILD-TYPE
  OTHER                                            2
  RADICAL HYSTERECTOMY                            91
  SIMPLE HYSTERECTOMY                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  3(2Q22.1) MUTATED              2          13          7
  DEL PEAK  3(2Q22.1) WILD-TYPE            6          27         33
D26V36, multiclass
              clus
vv             DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  CURRENT USER                           2                             6
  FORMER USER                           13                            27
  NEVER USED                             7                            33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V37, continuous
D26V38, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   13  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 60 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     13    0
  DEL PEAK  3(2Q22.1) WILD-TYPE   60   14
         clus
vv        DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  ABSENT                           13                            60
  PRESENT                           0                            14
[1] 2 2
[1] FALSE
D26V39, continuous
[1] "Remove cluster labels:"      "DEL PEAK  3(2Q22.1) MUTATED"
clus
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            2                             7 
                   TCGA-C5-A1MN                    TCGA-C5-A1MP 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-HM-A3JK 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-JW-A852                    TCGA-MU-A51Y 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-MU-A8JM 
"DEL PEAK  3(2Q22.1) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK  3(2Q22.1) MUTATED     0    0   6    9    3  0   2    1    2   1   1
  DEL PEAK  3(2Q22.1) WILD-TYPE   2    1  16   42   18  3   4    5    6  12   1
                               vv
clus                            T4 TX
  DEL PEAK  3(2Q22.1) MUTATED    0  1
  DEL PEAK  3(2Q22.1) WILD-TYPE  1  6
D26V40, multiclass
      clus
vv     DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1A                            0                             2
  T1A1                           0                             1
  T1B                            6                            16
  T1B1                           9                            42
  T1B2                           3                            18
  T2                             0                             3
  T2A                            2                             4
  T2A1                           1                             5
  T2A2                           2                             6
  T2B                            1                            12
  T3B                            1                             1
  T4                             0                             1
  TX                             1                             6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V41, continuous

Clustering(27) Variable = DEL PEAK  4(2Q37.1) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q37.1) MUTATED   55 12
  DEL PEAK  4(2Q37.1) WILD-TYPE 82 20
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                           67                           102 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                           12                            20 
$`DEL PEAK  4(2Q37.1) MUTATED`
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-A1BK TCGA-C5-A1BN TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A2LY 
      177.04         5.46        30.21        38.99        73.18        78.35 
TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7UE 
      100.14        52.01        18.02       182.93       134.33        85.55 
TCGA-C5-A7UH TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WH 
       60.69        87.75         2.66       117.99       118.65         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE 
        8.28         0.76        12.36         1.32        13.05         1.18 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A6QX TCGA-EA-A78R 
        1.35         1.81        12.66         0.26        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN 
       12.59        45.96         0.53         1.18         2.24         0.10 
TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A69L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI 
        0.10         7.92         4.47         0.92         0.66         1.45 
TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A770 TCGA-HM-A3JJ TCGA-IR-A3LK TCGA-IR-A3LL 
        0.82         1.35         1.12        21.67        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MY-A5BF 
       14.43        19.33        15.58         0.07         0.82         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        3.72         3.45         3.39        19.59         3.88        11.67 
TCGA-UC-A7PF 
       93.99 

$`DEL PEAK  4(2Q37.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
       49.48       144.16       173.29        82.85        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       31.40        46.32        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        0.46         2.43        40.93         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
       83.05        38.43         0.82        17.85        20.42        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UI 
      101.82        15.48         9.67        73.41        17.19        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A3LQ 
        9.34        13.61         2.73        58.88        36.76        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 
       16.83        16.18         1.74         0.82         0.62        14.50 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35        14.50        12.82        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB 
        0.69        14.99        14.96         6.64         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ 
        4.04         0.03         0.36        23.70         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K 
        0.03        20.35         6.94        14.70         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ 
       23.84         2.17         1.02         1.58         1.48         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.32         1.97        25.41        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU 
       81.96        16.64        20.48        10.06         5.13         0.10 
TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.89        13.87         0.03         5.42        29.72         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        2.96         5.85         3.72         5.75         4.80         6.25 

  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                       182.93                        173.29 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                        12.59                         14.50 
[1] "0.1 - 182.9 (12.6)" "0.0 - 173.3 (14.5)"
[1] "hr=" "1.2"
D27V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK  4(2Q37.1) MUTATED   42       11
  DEL PEAK  4(2Q37.1) WILD-TYPE 55       28
D27V3, multiclass
          clus
vv         DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  T1                                42                            55
  T2+T3+T4                          11                            28
[1] 2 2
[1] FALSE
D27V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   34 16
  DEL PEAK  4(2Q37.1) WILD-TYPE 53 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     34   16
  DEL PEAK  4(2Q37.1) WILD-TYPE   53   24
   clus
vv  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  0                          34                            53
  1                          16                            24
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  4(2Q37.1) MUTATED   30  0 25
  DEL PEAK  4(2Q37.1) WILD-TYPE 42  3 40
D27V5, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  M0                          30                            42
  M1                           0                             3
  MX                          25                            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"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q37.1) MUTATED               0                               63
  DEL PEAK  4(2Q37.1) WILD-TYPE             2                               81
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  4(2Q37.1) MUTATED                                               1
  DEL PEAK  4(2Q37.1) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  4(2Q37.1) MUTATED                                     4
  DEL PEAK  4(2Q37.1) WILD-TYPE                                  16
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  4(2Q37.1) MUTATED                                           0
  DEL PEAK  4(2Q37.1) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  4(2Q37.1) MUTATED                                              1
  DEL PEAK  4(2Q37.1) WILD-TYPE                                            3
D27V6, multiclass
                                               clus
vv                                              DEL PEAK  4(2Q37.1) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       63
  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                                              DEL PEAK  4(2Q37.1) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         81
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   11 58
  DEL PEAK  4(2Q37.1) WILD-TYPE 16 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     11   58
  DEL PEAK  4(2Q37.1) WILD-TYPE   16   91
     clus
vv    DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  NO                           11                            16
  YES                          58                            91
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.1) MUTATED                                  4     8
  DEL PEAK  4(2Q37.1) WILD-TYPE                                3     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(2Q37.1) MUTATED                           5
  DEL PEAK  4(2Q37.1) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(2Q37.1) MUTATED                                           0    51
  DEL PEAK  4(2Q37.1) WILD-TYPE                                         1    79
D27V10, multiclass
                                           clus
vv                                          DEL PEAK  4(2Q37.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    4
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              51
                                           clus
vv                                          DEL PEAK  4(2Q37.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED    3 52
  DEL PEAK  4(2Q37.1) WILD-TYPE  8 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED      3   52
  DEL PEAK  4(2Q37.1) WILD-TYPE    8   75
                        clus
vv                       DEL PEAK  4(2Q37.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       DEL PEAK  4(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            75
[1] 2 2
[1] FALSE
D27V12, continuous
D27V13, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   16 11
  DEL PEAK  4(2Q37.1) WILD-TYPE 32  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     16   11
  DEL PEAK  4(2Q37.1) WILD-TYPE   32    8
            clus
vv           DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  TUMOR FREE                          16                            32
  WITH TUMOR                          11                             8
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  4(2Q37.1) MUTATED         0      5       2            56       6
  DEL PEAK  4(2Q37.1) WILD-TYPE       1      5       4            91       6
D27V14, multiclass
               clus
vv              DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 2                             4
  UNITED STATES                          56                            91
  VIETNAM                                 6                             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                            G1 G2 G3 G4 GX
  DEL PEAK  4(2Q37.1) MUTATED    4 36 27  0  2
  DEL PEAK  4(2Q37.1) WILD-TYPE 10 47 45  1  3
D27V15, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  G1                           4                            10
  G2                          36                            47
  G3                          27                            45
  G4                           0                             1
  GX                           2                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V16, continuous
D27V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  4(2Q37.1) MUTATED                                             4
  DEL PEAK  4(2Q37.1) WILD-TYPE                                          17
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  4(2Q37.1) MUTATED                                        2
  DEL PEAK  4(2Q37.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  4(2Q37.1) MUTATED                                                 1
  DEL PEAK  4(2Q37.1) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  4(2Q37.1) MUTATED               12                  40
  DEL PEAK  4(2Q37.1) WILD-TYPE             24                  43
D27V18, multiclass
                                                 clus
vv                                                DEL PEAK  4(2Q37.1) 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                                                           12
  LIFELONG NON-SMOKER                                                      40
                                                 clus
vv                                                DEL PEAK  4(2Q37.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             24
  LIFELONG NON-SMOKER                                                        43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  4(2Q37.1) MUTATED             6       13             5        3
  DEL PEAK  4(2Q37.1) WILD-TYPE          11       24             6        2
D27V20, multiclass
               clus
vv              DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  COMBINATION                             6                            11
  EXTERNAL                               13                            24
  EXTERNAL BEAM                           5                             6
  INTERNAL                                3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V21, binary
                               cls
clus                            0 1
  DEL PEAK  4(2Q37.1) MUTATED   3 2
  DEL PEAK  4(2Q37.1) WILD-TYPE 8 1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED      3    2
  DEL PEAK  4(2Q37.1) WILD-TYPE    8    1
     clus
vv    DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  CGY                           3                             8
  GY                            2                             1
[1] 2 2
[1] FALSE
D27V22, continuous
D27V23, continuous
D27V24, continuous
D27V25, continuous
D27V26, continuous
D27V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  4(2Q37.1) MUTATED                                     0
  DEL PEAK  4(2Q37.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  4(2Q37.1) MUTATED                                     3
  DEL PEAK  4(2Q37.1) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  4(2Q37.1) MUTATED                         6                       1
  DEL PEAK  4(2Q37.1) WILD-TYPE                       3                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  4(2Q37.1) MUTATED                         0
  DEL PEAK  4(2Q37.1) WILD-TYPE                       5
D27V28, multiclass
                                     clus
vv                                    DEL PEAK  4(2Q37.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                       6
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    DEL PEAK  4(2Q37.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                         3
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK  4(2Q37.1) MUTATED                                               1
  DEL PEAK  4(2Q37.1) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  4(2Q37.1) MUTATED                                                5
  DEL PEAK  4(2Q37.1) WILD-TYPE                                              5
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  4(2Q37.1) MUTATED                                                                                  19
  DEL PEAK  4(2Q37.1) WILD-TYPE                                                                                35
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  4(2Q37.1) MUTATED                                                                                             30
  DEL PEAK  4(2Q37.1) WILD-TYPE                                                                                           47
D27V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  4(2Q37.1) 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)                                     19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          30
                                                                                              clus
vv                                                                                             DEL PEAK  4(2Q37.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V30, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   18 25
  DEL PEAK  4(2Q37.1) WILD-TYPE 36 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     18   25
  DEL PEAK  4(2Q37.1) WILD-TYPE   36   34
         clus
vv        DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  ABSENT                           18                            36
  PRESENT                          25                            34
[1] 2 2
[1] FALSE
D27V31, continuous
D27V32, continuous
D27V33, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   14 36
  DEL PEAK  4(2Q37.1) WILD-TYPE 21 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     14   36
  DEL PEAK  4(2Q37.1) WILD-TYPE   21   45
                                          clus
vv                                         DEL PEAK  4(2Q37.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          36
                                          clus
vv                                         DEL PEAK  4(2Q37.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            45
[1] 2 2
[1] FALSE
D27V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  4(2Q37.1) MUTATED       1                   45                   1
  DEL PEAK  4(2Q37.1) WILD-TYPE     2                   68                   4
D27V35, multiclass
                      clus
vv                     DEL PEAK  4(2Q37.1) MUTATED
  OTHER                                          1
  RADICAL HYSTERECTOMY                          45
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     DEL PEAK  4(2Q37.1) WILD-TYPE
  OTHER                                            2
  RADICAL HYSTERECTOMY                            68
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  4(2Q37.1) MUTATED              4          17         17
  DEL PEAK  4(2Q37.1) WILD-TYPE            4          23         23
D27V36, multiclass
              clus
vv             DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  CURRENT USER                           4                             4
  FORMER USER                           17                            23
  NEVER USED                            17                            23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V37, continuous
D27V38, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   27  4
  DEL PEAK  4(2Q37.1) WILD-TYPE 46 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     27    4
  DEL PEAK  4(2Q37.1) WILD-TYPE   46   10
         clus
vv        DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  ABSENT                           27                            46
  PRESENT                           4                            10
[1] 2 2
[1] FALSE
D27V39, continuous
[1] "Remove cluster labels:"      "DEL PEAK  4(2Q37.1) MUTATED"
clus
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                            2                             7 
                   TCGA-C5-A1MN                    TCGA-C5-A1MP 
"DEL PEAK  4(2Q37.1) WILD-TYPE" "DEL PEAK  4(2Q37.1) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-HM-A3JK 
"DEL PEAK  4(2Q37.1) WILD-TYPE" "DEL PEAK  4(2Q37.1) WILD-TYPE" 
                   TCGA-JW-A852                    TCGA-MU-A51Y 
"DEL PEAK  4(2Q37.1) WILD-TYPE" "DEL PEAK  4(2Q37.1) WILD-TYPE" 
                   TCGA-MU-A8JM 
"DEL PEAK  4(2Q37.1) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK  4(2Q37.1) MUTATED     1    0  12   23    6  0   2    1    5   2   0
  DEL PEAK  4(2Q37.1) WILD-TYPE   1    1  10   28   15  3   4    5    3  11   2
                               vv
clus                            T4 TX
  DEL PEAK  4(2Q37.1) MUTATED    1  3
  DEL PEAK  4(2Q37.1) WILD-TYPE  0  4
D27V40, multiclass
      clus
vv     DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  T1A                            1                             1
  T1A1                           0                             1
  T1B                           12                            10
  T1B1                          23                            28
  T1B2                           6                            15
  T2                             0                             3
  T2A                            2                             4
  T2A1                           1                             5
  T2A2                           5                             3
  T2B                            2                            11
  T3B                            0                             2
  T4                             1                             0
  TX                             3                             4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V41, continuous

Clustering(28) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q37.3) MUTATED   54 10
  DEL PEAK  5(2Q37.3) WILD-TYPE 83 22
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           64                           105 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           10                            22 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK 
       57.04        23.67        11.44        18.74        36.56       177.04 
TCGA-C5-A1BN TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ 
        5.46        30.21        38.99        73.18        78.35       100.14 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7UE TCGA-C5-A7UH TCGA-DR-A0ZL 
       52.01        18.02       182.93        85.55        60.69        87.75 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
        2.66       117.99       118.65         7.33         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A43B 
       12.36         1.32        13.05         1.18         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       12.66         0.26        13.58        13.48        12.59        45.96 
TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H6 
        0.53         1.18         2.24         0.10         0.10         7.92 
TCGA-EX-A69L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A40J 
        4.47         0.92         0.66         1.45         0.82         1.35 
TCGA-FU-A770 TCGA-HM-A3JJ TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VL 
        1.12        21.67        26.56        36.36        14.43        15.58 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        0.07         0.82         4.34         3.72         3.45         3.39 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       49.48        68.84       144.16       173.29        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        35.01        57.73        53.16 
TCGA-C5-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-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL 
       73.45        83.05        38.43         0.82        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       25.35       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM 
       17.19        94.95         9.34        13.61         2.73        58.88 
TCGA-DS-A0VK TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A3HQ TCGA-EA-A3HS 
       36.76        22.98        16.83        16.18         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A556 
        0.62        14.50         1.35        14.50        12.82        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2IP 
        1.48        13.91         0.69        14.99        14.96         6.64 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        0.59         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RO TCGA-EK-A3GJ 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-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ 
        6.12         1.22        23.84         2.17         1.02         1.58 
TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JK 
        1.48         3.52         1.32         1.97        25.41        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       96.95        78.71        81.96        16.64        19.33        20.48 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A51Y TCGA-MU-A5YI 
       10.06         5.13         0.10         0.89        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        5.42        29.72         0.07         2.96         5.85         3.72 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        5.75         4.80         6.25 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       182.93                        173.29 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       12.015                        14.700 
[1] "0.1 - 182.9 (12.0)" "0.0 - 173.3 (14.7)"
[1] "hr=" "1.2"
D28V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK  5(2Q37.3) MUTATED   41       10
  DEL PEAK  5(2Q37.3) WILD-TYPE 56       29
D28V3, multiclass
          clus
vv         DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  T1                                41                            56
  T2+T3+T4                          10                            29
[1] 2 2
[1] FALSE
D28V4, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   34 15
  DEL PEAK  5(2Q37.3) WILD-TYPE 53 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     34   15
  DEL PEAK  5(2Q37.3) WILD-TYPE   53   25
   clus
vv  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  0                          34                            53
  1                          15                            25
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  5(2Q37.3) MUTATED   30  0 23
  DEL PEAK  5(2Q37.3) WILD-TYPE 42  3 42
D28V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  M0                          30                            42
  M1                           0                             3
  MX                          23                            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"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED               0                               60
  DEL PEAK  5(2Q37.3) WILD-TYPE             2                               84
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  5(2Q37.3) MUTATED                                               1
  DEL PEAK  5(2Q37.3) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED                                     4
  DEL PEAK  5(2Q37.3) WILD-TYPE                                  16
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  5(2Q37.3) MUTATED                                           0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                         2
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  5(2Q37.3) MUTATED                                              1
  DEL PEAK  5(2Q37.3) WILD-TYPE                                            3
D28V6, multiclass
                                               clus
vv                                              DEL PEAK  5(2Q37.3) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       60
  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                                              DEL PEAK  5(2Q37.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   10 56
  DEL PEAK  5(2Q37.3) WILD-TYPE 17 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     10   56
  DEL PEAK  5(2Q37.3) WILD-TYPE   17   93
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                           10                            17
  YES                          56                            93
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q37.3) MUTATED                                  3     8
  DEL PEAK  5(2Q37.3) WILD-TYPE                                4     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q37.3) MUTATED                           5
  DEL PEAK  5(2Q37.3) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q37.3) MUTATED                                           0    49
  DEL PEAK  5(2Q37.3) WILD-TYPE                                         1    81
D28V10, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              49
                                           clus
vv                                          DEL PEAK  5(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                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"
D28V11, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED    2 52
  DEL PEAK  5(2Q37.3) WILD-TYPE  9 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      2   52
  DEL PEAK  5(2Q37.3) WILD-TYPE    9   75
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            75
[1] 2 2
[1] FALSE
D28V12, continuous
D28V13, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   16  9
  DEL PEAK  5(2Q37.3) WILD-TYPE 32 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     16    9
  DEL PEAK  5(2Q37.3) WILD-TYPE   32   10
            clus
vv           DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  TUMOR FREE                          16                            32
  WITH TUMOR                           9                            10
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  5(2Q37.3) MUTATED         0      5       2            53       6
  DEL PEAK  5(2Q37.3) WILD-TYPE       1      5       4            94       6
D28V14, multiclass
               clus
vv              DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 2                             4
  UNITED STATES                          53                            94
  VIETNAM                                 6                             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                            G1 G2 G3 G4 GX
  DEL PEAK  5(2Q37.3) MUTATED    4 34 26  0  2
  DEL PEAK  5(2Q37.3) WILD-TYPE 10 49 46  1  3
D28V15, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  G1                           4                            10
  G2                          34                            49
  G3                          26                            46
  G4                           0                             1
  GX                           2                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V16, continuous
D28V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  5(2Q37.3) MUTATED                                             4
  DEL PEAK  5(2Q37.3) WILD-TYPE                                          17
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  5(2Q37.3) MUTATED                                        1
  DEL PEAK  5(2Q37.3) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  5(2Q37.3) MUTATED                                                 0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  5(2Q37.3) MUTATED               12                  39
  DEL PEAK  5(2Q37.3) WILD-TYPE             24                  44
D28V18, multiclass
                                                 clus
vv                                                DEL PEAK  5(2Q37.3) 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                                                           12
  LIFELONG NON-SMOKER                                                      39
                                                 clus
vv                                                DEL PEAK  5(2Q37.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             24
  LIFELONG NON-SMOKER                                                        44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  5(2Q37.3) MUTATED             5       12             5        3
  DEL PEAK  5(2Q37.3) WILD-TYPE          12       25             6        2
D28V20, multiclass
               clus
vv              DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  COMBINATION                             5                            12
  EXTERNAL                               12                            25
  EXTERNAL BEAM                           5                             6
  INTERNAL                                3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V21, binary
                               cls
clus                            0 1
  DEL PEAK  5(2Q37.3) MUTATED   3 2
  DEL PEAK  5(2Q37.3) WILD-TYPE 8 1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      3    2
  DEL PEAK  5(2Q37.3) WILD-TYPE    8    1
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  CGY                           3                             8
  GY                            2                             1
[1] 2 2
[1] FALSE
D28V22, continuous
D28V23, continuous
D28V24, continuous
D28V25, continuous
D28V26, continuous
D28V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  5(2Q37.3) MUTATED                                     0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  5(2Q37.3) MUTATED                                     3
  DEL PEAK  5(2Q37.3) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  5(2Q37.3) MUTATED                         5                       1
  DEL PEAK  5(2Q37.3) WILD-TYPE                       4                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  5(2Q37.3) MUTATED                         0
  DEL PEAK  5(2Q37.3) WILD-TYPE                       5
D28V28, multiclass
                                     clus
vv                                    DEL PEAK  5(2Q37.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                       5
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    DEL PEAK  5(2Q37.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                         4
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK  5(2Q37.3) MUTATED                                               1
  DEL PEAK  5(2Q37.3) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  5(2Q37.3) MUTATED                                                5
  DEL PEAK  5(2Q37.3) WILD-TYPE                                              5
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  5(2Q37.3) MUTATED                                                                                  17
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                                                37
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  5(2Q37.3) MUTATED                                                                                             30
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                                                           47
D28V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  5(2Q37.3) 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)                          30
                                                                                              clus
vv                                                                                             DEL PEAK  5(2Q37.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       37
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V30, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   18 24
  DEL PEAK  5(2Q37.3) WILD-TYPE 36 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     18   24
  DEL PEAK  5(2Q37.3) WILD-TYPE   36   35
         clus
vv        DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  ABSENT                           18                            36
  PRESENT                          24                            35
[1] 2 2
[1] FALSE
D28V31, continuous
D28V32, continuous
D28V33, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   13 34
  DEL PEAK  5(2Q37.3) WILD-TYPE 22 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     13   34
  DEL PEAK  5(2Q37.3) WILD-TYPE   22   47
                                          clus
vv                                         DEL PEAK  5(2Q37.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          34
                                          clus
vv                                         DEL PEAK  5(2Q37.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            47
[1] 2 2
[1] FALSE
D28V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  5(2Q37.3) MUTATED       1                   44                   1
  DEL PEAK  5(2Q37.3) WILD-TYPE     2                   69                   4
D28V35, multiclass
                      clus
vv                     DEL PEAK  5(2Q37.3) MUTATED
  OTHER                                          1
  RADICAL HYSTERECTOMY                          44
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     DEL PEAK  5(2Q37.3) WILD-TYPE
  OTHER                                            2
  RADICAL HYSTERECTOMY                            69
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  5(2Q37.3) MUTATED              4          17         16
  DEL PEAK  5(2Q37.3) WILD-TYPE            4          23         24
D28V36, multiclass
              clus
vv             DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  CURRENT USER                           4                             4
  FORMER USER                           17                            23
  NEVER USED                            16                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V37, continuous
D28V38, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   27  3
  DEL PEAK  5(2Q37.3) WILD-TYPE 46 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     27    3
  DEL PEAK  5(2Q37.3) WILD-TYPE   46   11
         clus
vv        DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  ABSENT                           27                            46
  PRESENT                           3                            11
[1] 2 2
[1] FALSE
D28V39, continuous
[1] "Remove cluster labels:"      "DEL PEAK  5(2Q37.3) MUTATED"
clus
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                            2                             7 
                   TCGA-C5-A1MN                    TCGA-C5-A1MP 
"DEL PEAK  5(2Q37.3) WILD-TYPE" "DEL PEAK  5(2Q37.3) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-HM-A3JK 
"DEL PEAK  5(2Q37.3) WILD-TYPE" "DEL PEAK  5(2Q37.3) WILD-TYPE" 
                   TCGA-JW-A852                    TCGA-MU-A51Y 
"DEL PEAK  5(2Q37.3) WILD-TYPE" "DEL PEAK  5(2Q37.3) WILD-TYPE" 
                   TCGA-MU-A8JM 
"DEL PEAK  5(2Q37.3) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK  5(2Q37.3) MUTATED     1    0  11   23    6  0   2    1    5   1   0
  DEL PEAK  5(2Q37.3) WILD-TYPE   1    1  11   28   15  3   4    5    3  12   2
                               vv
clus                            T4 TX
  DEL PEAK  5(2Q37.3) MUTATED    1  3
  DEL PEAK  5(2Q37.3) WILD-TYPE  0  4
D28V40, multiclass
      clus
vv     DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  T1A                            1                             1
  T1A1                           0                             1
  T1B                           11                            11
  T1B1                          23                            28
  T1B2                           6                            15
  T2                             0                             3
  T2A                            2                             4
  T2A1                           1                             5
  T2A2                           5                             3
  T2B                            1                            12
  T3B                            0                             2
  T4                             1                             0
  TX                             3                             4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V41, continuous

Clustering(29) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(3P14.2) MUTATED   55 15
  DEL PEAK  6(3P14.2) WILD-TYPE 82 17
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           70                            99 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           15                            17 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        23.67        11.44        18.74        36.56       144.16 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MI 
      173.29         5.46        31.40        30.21        53.16        35.61 
TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7CJ 
       40.93        73.18        83.05        52.01        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
      134.33        15.48        73.41        85.55        60.69        94.95 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       13.61         2.73        87.75        36.76       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE 
       16.83         7.33        12.36         0.82        13.05         1.18 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5ZE 
        1.35        14.50        12.66         0.26        14.89        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       14.96        13.58        12.59        45.96         6.64         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EX-A1H5 TCGA-FU-A23L 
        0.59         0.07         4.04         0.36        20.35        23.84 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ 
        0.66         1.45         3.52         1.97        25.41        21.67 
TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-MU-A5YI 
      147.39        78.71        26.56        16.64        19.33         0.03 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-RA-A741 TCGA-UC-A7PF 
        3.45         3.39         3.88        93.99 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
       57.04        68.84       177.04        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK 
       46.32        35.01        57.73        38.99         0.46         2.43 
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-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CM 
        0.82        18.02        17.85        20.42       182.93         9.67 
TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WF 
       17.19         9.34        58.88         2.66        22.98        16.18 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3Y4 
        8.28         0.76         1.74         1.32         0.62        14.50 
TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
        1.35         1.81        12.82         1.48        13.91         0.69 
TCGA-EA-A78R TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
       13.48         0.03         1.18        23.70         2.24         0.10 
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-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         4.47         6.12         1.22         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A57G 
        1.02         1.58         1.48         0.82         1.35         1.32 
TCGA-FU-A770 TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
        1.12        20.78        14.93         4.11       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VK 
      117.40        96.95        81.96        36.36        14.43        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.82        13.87         5.42        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        2.96         3.72         5.85         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD 
        6.25        19.59        11.67 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       173.29                        182.93 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       17.785                         6.940 
[1] "0.0 - 173.3 (17.8)" "0.0 - 182.9 (6.9)" 
[1] "hr=" "1.3"
D29V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK  6(3P14.2) MUTATED   37       13
  DEL PEAK  6(3P14.2) WILD-TYPE 60       26
D29V3, multiclass
          clus
vv         DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  T1                                37                            60
  T2+T3+T4                          13                            26
[1] 2 2
[1] FALSE
D29V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   26 21
  DEL PEAK  6(3P14.2) WILD-TYPE 61 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     26   21
  DEL PEAK  6(3P14.2) WILD-TYPE   61   19
   clus
vv  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  0                          26                            61
  1                          21                            19
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  6(3P14.2) MUTATED   30  0 23
  DEL PEAK  6(3P14.2) WILD-TYPE 42  3 42
D29V5, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  M0                          30                            42
  M1                           0                             3
  MX                          23                            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"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(3P14.2) MUTATED               0                               71
  DEL PEAK  6(3P14.2) WILD-TYPE             2                               73
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  6(3P14.2) MUTATED                                               0
  DEL PEAK  6(3P14.2) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  6(3P14.2) MUTATED                                     1
  DEL PEAK  6(3P14.2) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  6(3P14.2) MUTATED                                           1
  DEL PEAK  6(3P14.2) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  6(3P14.2) MUTATED                                              1
  DEL PEAK  6(3P14.2) WILD-TYPE                                            3
D29V6, multiclass
                                               clus
vv                                              DEL PEAK  6(3P14.2) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       71
  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                                              DEL PEAK  6(3P14.2) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         73
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   16 58
  DEL PEAK  6(3P14.2) WILD-TYPE 11 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     16   58
  DEL PEAK  6(3P14.2) WILD-TYPE   11   91
     clus
vv    DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  NO                           16                            11
  YES                          58                            91
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P14.2) MUTATED                                  2     7
  DEL PEAK  6(3P14.2) WILD-TYPE                                5     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(3P14.2) MUTATED                           9
  DEL PEAK  6(3P14.2) WILD-TYPE                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(3P14.2) MUTATED                                           0    54
  DEL PEAK  6(3P14.2) WILD-TYPE                                         1    76
D29V10, multiclass
                                           clus
vv                                          DEL PEAK  6(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              54
                                           clus
vv                                          DEL PEAK  6(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                 8
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                76
[1] 5 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
  DEL PEAK  6(3P14.2) MUTATED    2 54
  DEL PEAK  6(3P14.2) WILD-TYPE  9 73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED      2   54
  DEL PEAK  6(3P14.2) WILD-TYPE    9   73
                        clus
vv                       DEL PEAK  6(3P14.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK  6(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            73
[1] 2 2
[1] FALSE
D29V12, continuous
D29V13, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   23 10
  DEL PEAK  6(3P14.2) WILD-TYPE 25  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     23   10
  DEL PEAK  6(3P14.2) WILD-TYPE   25    9
            clus
vv           DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  TUMOR FREE                          23                            25
  WITH TUMOR                          10                             9
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  6(3P14.2) MUTATED         0      5       1            62       6
  DEL PEAK  6(3P14.2) WILD-TYPE       1      5       5            85       6
D29V14, multiclass
               clus
vv              DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 1                             5
  UNITED STATES                          62                            85
  VIETNAM                                 6                             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                            G1 G2 G3 G4 GX
  DEL PEAK  6(3P14.2) MUTATED    3 34 33  1  2
  DEL PEAK  6(3P14.2) WILD-TYPE 11 49 39  0  3
D29V15, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  G1                           3                            11
  G2                          34                            49
  G3                          33                            39
  G4                           1                             0
  GX                           2                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V16, continuous
D29V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  6(3P14.2) MUTATED                                             9
  DEL PEAK  6(3P14.2) WILD-TYPE                                          12
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  6(3P14.2) MUTATED                                        2
  DEL PEAK  6(3P14.2) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  6(3P14.2) MUTATED                                                 1
  DEL PEAK  6(3P14.2) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  6(3P14.2) MUTATED               23                  26
  DEL PEAK  6(3P14.2) WILD-TYPE             13                  57
D29V18, multiclass
                                                 clus
vv                                                DEL PEAK  6(3P14.2) 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                                                           23
  LIFELONG NON-SMOKER                                                      26
                                                 clus
vv                                                DEL PEAK  6(3P14.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             13
  LIFELONG NON-SMOKER                                                        57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  6(3P14.2) MUTATED            10       14             6        4
  DEL PEAK  6(3P14.2) WILD-TYPE           7       23             5        1
D29V20, multiclass
               clus
vv              DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  COMBINATION                            10                             7
  EXTERNAL                               14                            23
  EXTERNAL BEAM                           6                             5
  INTERNAL                                4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V21, binary
                               cls
clus                            0 1
  DEL PEAK  6(3P14.2) MUTATED   5 2
  DEL PEAK  6(3P14.2) WILD-TYPE 6 1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED      5    2
  DEL PEAK  6(3P14.2) WILD-TYPE    6    1
     clus
vv    DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  CGY                           5                             6
  GY                            2                             1
[1] 2 2
[1] FALSE
D29V22, continuous
D29V23, continuous
D29V24, continuous
D29V25, continuous
D29V26, continuous
D29V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  6(3P14.2) MUTATED                                     0
  DEL PEAK  6(3P14.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  6(3P14.2) MUTATED                                     4
  DEL PEAK  6(3P14.2) WILD-TYPE                                   2
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  6(3P14.2) MUTATED                         2                       1
  DEL PEAK  6(3P14.2) WILD-TYPE                       7                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  6(3P14.2) MUTATED                         3
  DEL PEAK  6(3P14.2) WILD-TYPE                       2
D29V28, multiclass
                                     clus
vv                                    DEL PEAK  6(3P14.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                       2
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       3
                                     clus
vv                                    DEL PEAK  6(3P14.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                         7
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK  6(3P14.2) MUTATED                                               1
  DEL PEAK  6(3P14.2) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  6(3P14.2) MUTATED                                                4
  DEL PEAK  6(3P14.2) WILD-TYPE                                              6
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  6(3P14.2) MUTATED                                                                                  20
  DEL PEAK  6(3P14.2) WILD-TYPE                                                                                34
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  6(3P14.2) MUTATED                                                                                             31
  DEL PEAK  6(3P14.2) WILD-TYPE                                                                                           46
D29V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  6(3P14.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          31
                                                                                              clus
vv                                                                                             DEL PEAK  6(3P14.2) 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)                                       34
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V30, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   13 28
  DEL PEAK  6(3P14.2) WILD-TYPE 41 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     13   28
  DEL PEAK  6(3P14.2) WILD-TYPE   41   31
         clus
vv        DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  ABSENT                           13                            41
  PRESENT                          28                            31
[1] 2 2
[1] FALSE
D29V31, continuous
D29V32, continuous
D29V33, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   18 33
  DEL PEAK  6(3P14.2) WILD-TYPE 17 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     18   33
  DEL PEAK  6(3P14.2) WILD-TYPE   17   48
                                          clus
vv                                         DEL PEAK  6(3P14.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          33
                                          clus
vv                                         DEL PEAK  6(3P14.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            48
[1] 2 2
[1] FALSE
D29V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  6(3P14.2) MUTATED       0                   46                   0
  DEL PEAK  6(3P14.2) WILD-TYPE     3                   67                   5
D29V35, multiclass
                      clus
vv                     DEL PEAK  6(3P14.2) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          46
  SIMPLE HYSTERECTOMY                            0
                      clus
vv                     DEL PEAK  6(3P14.2) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            67
  SIMPLE HYSTERECTOMY                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  6(3P14.2) MUTATED              2          22         13
  DEL PEAK  6(3P14.2) WILD-TYPE            6          18         27
D29V36, multiclass
              clus
vv             DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  CURRENT USER                           2                             6
  FORMER USER                           22                            18
  NEVER USED                            13                            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V37, continuous
D29V38, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   26  7
  DEL PEAK  6(3P14.2) WILD-TYPE 47  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     26    7
  DEL PEAK  6(3P14.2) WILD-TYPE   47    7
         clus
vv        DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  ABSENT                           26                            47
  PRESENT                           7                             7
[1] 2 2
[1] FALSE
D29V39, continuous
[1] "Remove cluster labels:"      "DEL PEAK  6(3P14.2) MUTATED"
clus
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                            2                             7 
                   TCGA-C5-A1MH                    TCGA-C5-A1MP 
"DEL PEAK  6(3P14.2) WILD-TYPE" "DEL PEAK  6(3P14.2) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-HM-A3JK 
"DEL PEAK  6(3P14.2) WILD-TYPE" "DEL PEAK  6(3P14.2) WILD-TYPE" 
                   TCGA-JW-A852                    TCGA-MU-A51Y 
"DEL PEAK  6(3P14.2) WILD-TYPE" "DEL PEAK  6(3P14.2) WILD-TYPE" 
                   TCGA-MU-A8JM 
"DEL PEAK  6(3P14.2) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK  6(3P14.2) MUTATED     0    1   9   21    6  1   2    3    2   4   0
  DEL PEAK  6(3P14.2) WILD-TYPE   2    0  13   30   15  2   4    3    6   9   2
                               vv
clus                            T4 TX
  DEL PEAK  6(3P14.2) MUTATED    1  3
  DEL PEAK  6(3P14.2) WILD-TYPE  0  4
D29V40, multiclass
      clus
vv     DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  T1A                            0                             2
  T1A1                           1                             0
  T1B                            9                            13
  T1B1                          21                            30
  T1B2                           6                            15
  T2                             1                             2
  T2A                            2                             4
  T2A1                           3                             3
  T2A2                           2                             6
  T2B                            4                             9
  T3B                            0                             2
  T4                             1                             0
  TX                             3                             4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V41, continuous

Clustering(30) Variable = DEL PEAK  7(4Q21.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q21.3) MUTATED    35  13
  DEL PEAK  7(4Q21.3) WILD-TYPE 102  19
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                           48                           121 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                           13                            19 
$`DEL PEAK  7(4Q21.3) MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BN TCGA-C5-A1M6 
       49.48        23.67        11.44        68.84         5.46        31.40 
TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE 
       35.61        73.18        73.45        83.05        52.01        18.02 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
      134.33        15.48         9.67        73.41        17.19        60.69 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A1QT 
        9.34        13.61         2.73        87.75       118.65        12.36 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5ZD 
        1.35        14.50         1.81         0.26        14.89         0.69 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM 
       13.48        12.59         0.53         0.59         1.18         2.24 
TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A3NI TCGA-FU-A5XV TCGA-HM-A3JJ 
        0.10        20.35         6.94         1.45         1.97        21.67 
TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AW TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD 
       20.48         0.10         0.89         2.96         3.45        11.67 

$`DEL PEAK  7(4Q21.3) WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       57.04        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       82.85        19.86        67.46        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       57.73        53.16        38.99         0.46         2.43        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
        3.58        44.22        78.35       100.14        38.43         0.82 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UE 
       17.85        20.42       182.93        25.35       101.82        85.55 
TCGA-C5-A7UI TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       94.95        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         7.33         8.28         0.76         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZE 
        1.35        12.66        12.82         1.48        13.91        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC 
       14.96        13.58        45.96         6.64         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.03         0.36        23.70         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        0.03         7.92        14.70         4.47         6.12         1.22 
TCGA-FU-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-A40J TCGA-FU-A57G TCGA-FU-A770 
        1.48         0.82         3.52         1.35         1.32         1.12 
TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       25.41        20.78        14.93         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        14.43        16.64        19.33        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        5.13         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       29.72         0.07         4.34         3.72         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PF 
       93.99 

  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                       134.33                        182.93 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                       13.035                        13.870 
[1] "0.1 - 134.3 (13.0)" "0.0 - 182.9 (13.9)"
[1] "hr=" "1.9"
D30V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK  7(4Q21.3) MUTATED   25       10
  DEL PEAK  7(4Q21.3) WILD-TYPE 72       29
D30V3, multiclass
          clus
vv         DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  T1                                25                            72
  T2+T3+T4                          10                            29
[1] 2 2
[1] FALSE
D30V4, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q21.3) MUTATED   18 15
  DEL PEAK  7(4Q21.3) WILD-TYPE 69 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     18   15
  DEL PEAK  7(4Q21.3) WILD-TYPE   69   25
   clus
vv  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  0                          18                            69
  1                          15                            25
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  7(4Q21.3) MUTATED   23  0 13
  DEL PEAK  7(4Q21.3) WILD-TYPE 49  3 52
D30V5, multiclass
    clus
vv   DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  M0                          23                            49
  M1                           0                             3
  MX                          13                            52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(4Q21.3) MUTATED               0                               48
  DEL PEAK  7(4Q21.3) WILD-TYPE             2                               96
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  7(4Q21.3) MUTATED                                               1
  DEL PEAK  7(4Q21.3) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  7(4Q21.3) MUTATED                                     1
  DEL PEAK  7(4Q21.3) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  7(4Q21.3) MUTATED                                           1
  DEL PEAK  7(4Q21.3) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  7(4Q21.3) MUTATED                                              1
  DEL PEAK  7(4Q21.3) WILD-TYPE                                            3
D30V6, multiclass
                                               clus
vv                                              DEL PEAK  7(4Q21.3) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       48
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  7(4Q21.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         96
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED    10  42
  DEL PEAK  7(4Q21.3) WILD-TYPE  17 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     10   42
  DEL PEAK  7(4Q21.3) WILD-TYPE   17  107
     clus
vv    DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  NO                           10                            17
  YES                          42                           107
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(4Q21.3) MUTATED                                  1     7
  DEL PEAK  7(4Q21.3) WILD-TYPE                                6     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(4Q21.3) MUTATED                           9
  DEL PEAK  7(4Q21.3) WILD-TYPE                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(4Q21.3) MUTATED                                           0    35
  DEL PEAK  7(4Q21.3) WILD-TYPE                                         1    95
D30V10, multiclass
                                           clus
vv                                          DEL PEAK  7(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              35
                                           clus
vv                                          DEL PEAK  7(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                 8
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                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"
D30V11, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q21.3) MUTATED    2 41
  DEL PEAK  7(4Q21.3) WILD-TYPE  9 86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED      2   41
  DEL PEAK  7(4Q21.3) WILD-TYPE    9   86
                        clus
vv                       DEL PEAK  7(4Q21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       DEL PEAK  7(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            86
[1] 2 2
[1] FALSE
D30V12, continuous
D30V13, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q21.3) MUTATED   12  7
  DEL PEAK  7(4Q21.3) WILD-TYPE 36 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     12    7
  DEL PEAK  7(4Q21.3) WILD-TYPE   36   12
            clus
vv           DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  TUMOR FREE                          12                            36
  WITH TUMOR                           7                            12
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  7(4Q21.3) MUTATED         1      3       1            41       6
  DEL PEAK  7(4Q21.3) WILD-TYPE       0      7       5           106       6
D30V14, multiclass
               clus
vv              DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  NIGERIA                                 1                             0
  RUSSIA                                  3                             7
  UKRAINE                                 1                             5
  UNITED STATES                          41                           106
  VIETNAM                                 6                             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                            G1 G2 G3 G4 GX
  DEL PEAK  7(4Q21.3) MUTATED    1 22 29  0  0
  DEL PEAK  7(4Q21.3) WILD-TYPE 13 61 43  1  5
D30V15, multiclass
    clus
vv   DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  G1                           1                            13
  G2                          22                            61
  G3                          29                            43
  G4                           0                             1
  GX                           0                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V16, continuous
D30V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  7(4Q21.3) MUTATED                                             3
  DEL PEAK  7(4Q21.3) WILD-TYPE                                          18
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  7(4Q21.3) MUTATED                                        3
  DEL PEAK  7(4Q21.3) WILD-TYPE                                      5
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  7(4Q21.3) MUTATED                                                 1
  DEL PEAK  7(4Q21.3) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  7(4Q21.3) MUTATED               12                  19
  DEL PEAK  7(4Q21.3) WILD-TYPE             24                  64
D30V18, multiclass
                                                 clus
vv                                                DEL PEAK  7(4Q21.3) 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                                                           12
  LIFELONG NON-SMOKER                                                      19
                                                 clus
vv                                                DEL PEAK  7(4Q21.3) 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                                                             24
  LIFELONG NON-SMOKER                                                        64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  7(4Q21.3) MUTATED             5        9             4        4
  DEL PEAK  7(4Q21.3) WILD-TYPE          12       28             7        1
D30V20, multiclass
               clus
vv              DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  COMBINATION                             5                            12
  EXTERNAL                                9                            28
  EXTERNAL BEAM                           4                             7
  INTERNAL                                4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V21, binary
                               cls
clus                            0 1
  DEL PEAK  7(4Q21.3) MUTATED   5 1
  DEL PEAK  7(4Q21.3) WILD-TYPE 6 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED      5    1
  DEL PEAK  7(4Q21.3) WILD-TYPE    6    2
     clus
vv    DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  CGY                           5                             6
  GY                            1                             2
[1] 2 2
[1] FALSE
D30V22, continuous
D30V23, continuous
D30V24, continuous
D30V25, continuous
D30V26, continuous
D30V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  7(4Q21.3) MUTATED                                     0
  DEL PEAK  7(4Q21.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  7(4Q21.3) MUTATED                                     3
  DEL PEAK  7(4Q21.3) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  7(4Q21.3) MUTATED                         4                       1
  DEL PEAK  7(4Q21.3) WILD-TYPE                       5                       0
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  7(4Q21.3) MUTATED                         1
  DEL PEAK  7(4Q21.3) WILD-TYPE                       4
D30V28, multiclass
                                     clus
vv                                    DEL PEAK  7(4Q21.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                       4
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  7(4Q21.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                         5
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK  7(4Q21.3) MUTATED                                               0
  DEL PEAK  7(4Q21.3) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  7(4Q21.3) MUTATED                                                3
  DEL PEAK  7(4Q21.3) WILD-TYPE                                              7
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  7(4Q21.3) MUTATED                                                                                  16
  DEL PEAK  7(4Q21.3) WILD-TYPE                                                                                38
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  7(4Q21.3) MUTATED                                                                                             19
  DEL PEAK  7(4Q21.3) WILD-TYPE                                                                                           58
D30V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  7(4Q21.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          19
                                                                                              clus
vv                                                                                             DEL PEAK  7(4Q21.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V30, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q21.3) MUTATED   10 20
  DEL PEAK  7(4Q21.3) WILD-TYPE 44 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     10   20
  DEL PEAK  7(4Q21.3) WILD-TYPE   44   39
         clus
vv        DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  ABSENT                           10                            44
  PRESENT                          20                            39
[1] 2 2
[1] FALSE
D30V31, continuous
D30V32, continuous
D30V33, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q21.3) MUTATED   13 25
  DEL PEAK  7(4Q21.3) WILD-TYPE 22 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     13   25
  DEL PEAK  7(4Q21.3) WILD-TYPE   22   56
                                          clus
vv                                         DEL PEAK  7(4Q21.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          25
                                          clus
vv                                         DEL PEAK  7(4Q21.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            56
[1] 2 2
[1] FALSE
D30V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  7(4Q21.3) MUTATED       0                   33                   1
  DEL PEAK  7(4Q21.3) WILD-TYPE     3                   80                   4
D30V35, multiclass
                      clus
vv                     DEL PEAK  7(4Q21.3) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          33
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     DEL PEAK  7(4Q21.3) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            80
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  7(4Q21.3) MUTATED              3          11          9
  DEL PEAK  7(4Q21.3) WILD-TYPE            5          29         31
D30V36, multiclass
              clus
vv             DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  CURRENT USER                           3                             5
  FORMER USER                           11                            29
  NEVER USED                             9                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V37, continuous
D30V38, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q21.3) MUTATED   15  5
  DEL PEAK  7(4Q21.3) WILD-TYPE 58  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     15    5
  DEL PEAK  7(4Q21.3) WILD-TYPE   58    9
         clus
vv        DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  ABSENT                           15                            58
  PRESENT                           5                             9
[1] 2 2
[1] FALSE
D30V39, continuous
[1] "Remove cluster labels:"      "DEL PEAK  7(4Q21.3) MUTATED"
clus
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                            1                             8 
                   TCGA-C5-A1MH                    TCGA-C5-A1MN 
"DEL PEAK  7(4Q21.3) WILD-TYPE" "DEL PEAK  7(4Q21.3) WILD-TYPE" 
                   TCGA-C5-A1MP                    TCGA-EK-A2RO 
"DEL PEAK  7(4Q21.3) WILD-TYPE" "DEL PEAK  7(4Q21.3) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-JW-A852 
"DEL PEAK  7(4Q21.3) WILD-TYPE" "DEL PEAK  7(4Q21.3) WILD-TYPE" 
                   TCGA-MU-A51Y                    TCGA-MU-A8JM 
"DEL PEAK  7(4Q21.3) WILD-TYPE" "DEL PEAK  7(4Q21.3) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK  7(4Q21.3) MUTATED     1    0   7   12    5  2   1    2    0   4   0
  DEL PEAK  7(4Q21.3) WILD-TYPE   1    1  15   39   16  1   5    4    8   9   2
                               vv
clus                            T4 TX
  DEL PEAK  7(4Q21.3) MUTATED    1  1
  DEL PEAK  7(4Q21.3) WILD-TYPE  0  6
D30V40, multiclass
      clus
vv     DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  T1A                            1                             1
  T1A1                           0                             1
  T1B                            7                            15
  T1B1                          12                            39
  T1B2                           5                            16
  T2                             2                             1
  T2A                            1                             5
  T2A1                           2                             4
  T2A2                           0                             8
  T2B                            4                             9
  T3B                            0                             2
  T4                             1                             0
  TX                             1                             6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V41, continuous

Clustering(31) Variable = DEL PEAK  8(4Q22.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q22.1) MUTATED    34  11
  DEL PEAK  8(4Q22.1) WILD-TYPE 103  21
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           45                           124 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           11                            21 
$`DEL PEAK  8(4Q22.1) MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MI 
       49.48        23.67        11.44         5.46        31.40        35.61 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL 
       73.18        73.45        83.05        52.01        18.02        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
        9.67        73.41        17.19        60.69         9.34        13.61 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        2.73        87.75        12.36         1.35        14.50         1.81 
TCGA-EA-A556 TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 
       14.89        13.48        12.59        45.96         0.53         0.59 
TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A3NI 
        1.18         2.24         0.10        20.35         6.94         1.45 
TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-IR-A3LK TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AW 
        1.97        21.67        26.56        20.48         0.10         0.89 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD 
        2.96         3.45        11.67 

$`DEL PEAK  8(4Q22.1) 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-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK 
       35.01        57.73        53.16        38.99         0.46         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       40.93         3.58        44.22        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
        0.82        17.85        20.42       182.93        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7UE TCGA-C5-A7UI TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
      134.33        85.55        94.95        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-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-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-A5ZF 
        0.26         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
       13.58         6.64         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-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK 
        3.52         1.35         1.32         1.12        25.41        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       96.95        78.71        81.96        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AX TCGA-LP-A5U3 
       19.33        15.58        10.06         5.13         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.72         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        6.25        19.59         3.88        93.99 

  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                        87.75                        182.93 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                       13.480                        13.725 
[1] "0.1 - 87.8 (13.5)"  "0.0 - 182.9 (13.7)"
[1] "hr=" "2"  
D31V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK  8(4Q22.1) MUTATED   23        9
  DEL PEAK  8(4Q22.1) WILD-TYPE 74       30
D31V3, multiclass
          clus
vv         DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  T1                                23                            74
  T2+T3+T4                           9                            30
[1] 2 2
[1] FALSE
D31V4, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   17 13
  DEL PEAK  8(4Q22.1) WILD-TYPE 70 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     17   13
  DEL PEAK  8(4Q22.1) WILD-TYPE   70   27
   clus
vv  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  0                          17                            70
  1                          13                            27
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  8(4Q22.1) MUTATED   21  0 12
  DEL PEAK  8(4Q22.1) WILD-TYPE 51  3 53
D31V5, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  M0                          21                            51
  M1                           0                             3
  MX                          12                            53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(4Q22.1) MUTATED               0                               45
  DEL PEAK  8(4Q22.1) WILD-TYPE             2                               99
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  8(4Q22.1) MUTATED                                               1
  DEL PEAK  8(4Q22.1) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  8(4Q22.1) MUTATED                                     1
  DEL PEAK  8(4Q22.1) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  8(4Q22.1) MUTATED                                           1
  DEL PEAK  8(4Q22.1) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  8(4Q22.1) MUTATED                                              1
  DEL PEAK  8(4Q22.1) WILD-TYPE                                            3
D31V6, multiclass
                                               clus
vv                                              DEL PEAK  8(4Q22.1) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       45
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  8(4Q22.1) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         99
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.1) MUTATED     8  41
  DEL PEAK  8(4Q22.1) WILD-TYPE  19 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED      8   41
  DEL PEAK  8(4Q22.1) WILD-TYPE   19  108
     clus
vv    DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  NO                            8                            19
  YES                          41                           108
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4Q22.1) MUTATED                                  1     5
  DEL PEAK  8(4Q22.1) WILD-TYPE                                6    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(4Q22.1) MUTATED                           9
  DEL PEAK  8(4Q22.1) WILD-TYPE                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(4Q22.1) MUTATED                                           0    34
  DEL PEAK  8(4Q22.1) WILD-TYPE                                         1    96
D31V10, multiclass
                                           clus
vv                                          DEL PEAK  8(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              34
                                           clus
vv                                          DEL PEAK  8(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                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"
D31V11, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED    2 38
  DEL PEAK  8(4Q22.1) WILD-TYPE  9 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED      2   38
  DEL PEAK  8(4Q22.1) WILD-TYPE    9   89
                        clus
vv                       DEL PEAK  8(4Q22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          38
                        clus
vv                       DEL PEAK  8(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            89
[1] 2 2
[1] FALSE
D31V12, continuous
D31V13, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   11  6
  DEL PEAK  8(4Q22.1) WILD-TYPE 37 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     11    6
  DEL PEAK  8(4Q22.1) WILD-TYPE   37   13
            clus
vv           DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  TUMOR FREE                          11                            37
  WITH TUMOR                           6                            13
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  8(4Q22.1) MUTATED         1      3       1            40       4
  DEL PEAK  8(4Q22.1) WILD-TYPE       0      7       5           107       8
D31V14, multiclass
               clus
vv              DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  NIGERIA                                 1                             0
  RUSSIA                                  3                             7
  UKRAINE                                 1                             5
  UNITED STATES                          40                           107
  VIETNAM                                 4                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK  8(4Q22.1) MUTATED    1 17 31  0  0
  DEL PEAK  8(4Q22.1) WILD-TYPE 13 66 41  1  5
D31V15, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  G1                           1                            13
  G2                          17                            66
  G3                          31                            41
  G4                           0                             1
  GX                           0                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V16, continuous
D31V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  8(4Q22.1) MUTATED                                             3
  DEL PEAK  8(4Q22.1) WILD-TYPE                                          18
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  8(4Q22.1) MUTATED                                        2
  DEL PEAK  8(4Q22.1) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  8(4Q22.1) MUTATED                                                 0
  DEL PEAK  8(4Q22.1) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  8(4Q22.1) MUTATED               12                  17
  DEL PEAK  8(4Q22.1) WILD-TYPE             24                  66
D31V18, multiclass
                                                 clus
vv                                                DEL PEAK  8(4Q22.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           12
  LIFELONG NON-SMOKER                                                      17
                                                 clus
vv                                                DEL PEAK  8(4Q22.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             24
  LIFELONG NON-SMOKER                                                        66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  8(4Q22.1) MUTATED             4        9             3        4
  DEL PEAK  8(4Q22.1) WILD-TYPE          13       28             8        1
D31V20, multiclass
               clus
vv              DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  COMBINATION                             4                            13
  EXTERNAL                                9                            28
  EXTERNAL BEAM                           3                             8
  INTERNAL                                4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V21, binary
                               cls
clus                            0 1
  DEL PEAK  8(4Q22.1) MUTATED   5 1
  DEL PEAK  8(4Q22.1) WILD-TYPE 6 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED      5    1
  DEL PEAK  8(4Q22.1) WILD-TYPE    6    2
     clus
vv    DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  CGY                           5                             6
  GY                            1                             2
[1] 2 2
[1] FALSE
D31V22, continuous
D31V23, continuous
D31V24, continuous
D31V25, continuous
D31V26, continuous
D31V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  8(4Q22.1) MUTATED                                     0
  DEL PEAK  8(4Q22.1) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  8(4Q22.1) MUTATED                                     4
  DEL PEAK  8(4Q22.1) WILD-TYPE                                   2
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  8(4Q22.1) MUTATED                         2                       0
  DEL PEAK  8(4Q22.1) WILD-TYPE                       7                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  8(4Q22.1) MUTATED                         1
  DEL PEAK  8(4Q22.1) WILD-TYPE                       4
D31V28, multiclass
                                     clus
vv                                    DEL PEAK  8(4Q22.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                       2
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  8(4Q22.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                         7
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK  8(4Q22.1) MUTATED                                               0
  DEL PEAK  8(4Q22.1) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  8(4Q22.1) MUTATED                                                3
  DEL PEAK  8(4Q22.1) WILD-TYPE                                              7
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  8(4Q22.1) MUTATED                                                                                  16
  DEL PEAK  8(4Q22.1) WILD-TYPE                                                                                38
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  8(4Q22.1) MUTATED                                                                                             17
  DEL PEAK  8(4Q22.1) WILD-TYPE                                                                                           60
D31V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  8(4Q22.1) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          17
                                                                                              clus
vv                                                                                             DEL PEAK  8(4Q22.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V30, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED    8 18
  DEL PEAK  8(4Q22.1) WILD-TYPE 46 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED      8   18
  DEL PEAK  8(4Q22.1) WILD-TYPE   46   41
         clus
vv        DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  ABSENT                            8                            46
  PRESENT                          18                            41
[1] 2 2
[1] FALSE
D31V31, continuous
D31V32, continuous
D31V33, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   11 23
  DEL PEAK  8(4Q22.1) WILD-TYPE 24 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     11   23
  DEL PEAK  8(4Q22.1) WILD-TYPE   24   58
                                          clus
vv                                         DEL PEAK  8(4Q22.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          23
                                          clus
vv                                         DEL PEAK  8(4Q22.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            58
[1] 2 2
[1] FALSE
D31V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  8(4Q22.1) MUTATED       0                   30                   1
  DEL PEAK  8(4Q22.1) WILD-TYPE     3                   83                   4
D31V35, multiclass
                      clus
vv                     DEL PEAK  8(4Q22.1) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          30
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     DEL PEAK  8(4Q22.1) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            83
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  8(4Q22.1) MUTATED              3           9         10
  DEL PEAK  8(4Q22.1) WILD-TYPE            5          31         30
D31V36, multiclass
              clus
vv             DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  CURRENT USER                           3                             5
  FORMER USER                            9                            31
  NEVER USED                            10                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V37, continuous
D31V38, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   14  3
  DEL PEAK  8(4Q22.1) WILD-TYPE 59 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     14    3
  DEL PEAK  8(4Q22.1) WILD-TYPE   59   11
         clus
vv        DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  ABSENT                           14                            59
  PRESENT                           3                            11
[1] 2 2
[1] FALSE
D31V39, continuous
[1] "Remove cluster labels:"      "DEL PEAK  8(4Q22.1) MUTATED"
clus
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                            1                             8 
                   TCGA-C5-A1MH                    TCGA-C5-A1MN 
"DEL PEAK  8(4Q22.1) WILD-TYPE" "DEL PEAK  8(4Q22.1) WILD-TYPE" 
                   TCGA-C5-A1MP                    TCGA-EK-A2RO 
"DEL PEAK  8(4Q22.1) WILD-TYPE" "DEL PEAK  8(4Q22.1) WILD-TYPE" 
                   TCGA-HM-A3JK                    TCGA-JW-A852 
"DEL PEAK  8(4Q22.1) WILD-TYPE" "DEL PEAK  8(4Q22.1) WILD-TYPE" 
                   TCGA-MU-A51Y                    TCGA-MU-A8JM 
"DEL PEAK  8(4Q22.1) WILD-TYPE" "DEL PEAK  8(4Q22.1) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK  8(4Q22.1) MUTATED     1    0   6   11    5  2   1    2    0   4   0
  DEL PEAK  8(4Q22.1) WILD-TYPE   1    1  16   40   16  1   5    4    8   9   2
                               vv
clus                            T4 TX
  DEL PEAK  8(4Q22.1) MUTATED    0  1
  DEL PEAK  8(4Q22.1) WILD-TYPE  1  6
D31V40, multiclass
      clus
vv     DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  T1A                            1                             1
  T1A1                           0                             1
  T1B                            6                            16
  T1B1                          11                            40
  T1B2                           5                            16
  T2                             2                             1
  T2A                            1                             5
  T2A1                           2                             4
  T2A2                           0                             8
  T2B                            4                             9
  T3B                            0                             2
  T4                             0                             1
  TX                             1                             6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V41, continuous

Clustering(32) Variable = DEL PEAK  9(4Q35.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(4Q35.2) MUTATED   47 13
  DEL PEAK  9(4Q35.2) WILD-TYPE 90 19
  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE 
                           60                           109 
  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE 
                           13                            19 
$`DEL PEAK  9(4Q35.2) MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
       57.04        23.67        11.44         5.46        67.46        31.40 
TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       57.73        35.61        40.93        73.18        73.45        83.05 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       52.01        18.02       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       17.19        60.69         9.34        13.61         2.73        87.75 
TCGA-DS-A5RQ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A411 
       16.83         0.76        12.36         0.62        13.05         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.50         1.81        12.66        14.89        14.99        14.96 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ 
       13.48        12.59        45.96         0.53         0.59         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A2QG TCGA-FU-A3NI 
        2.24         0.10        20.35         6.94         0.92         1.45 
TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-JW-A5VG TCGA-JW-A5VK TCGA-LP-A4AU 
        1.97        21.67       137.16        14.43        20.48         0.10 
TCGA-LP-A4AW TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD 
        0.89         2.96         3.45         6.25        19.59        11.67 

$`DEL PEAK  9(4Q35.2) 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-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
      173.29        82.85        19.86        46.32        30.21        35.01 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       53.16        38.99         0.46         2.43         3.58        44.22 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14        38.43         0.82        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UE TCGA-C5-A7UI TCGA-DR-A0ZM 
      182.93        25.35       101.82        85.55        94.95        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WF 
       36.76         2.66       117.99       118.65        22.98        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QE 
        7.33         8.28         1.74         1.32         0.82         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50         1.35        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        0.69        13.58         6.64         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.36        23.70         0.07         0.10         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        7.92        14.70         4.47         6.12         1.22        23.84 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-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-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         4.11       147.39        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ 
       78.71        81.96        26.56        36.36        16.64        19.33 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
       15.58        10.06         5.13         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
        0.03         5.42        29.72         0.07         4.34         3.72 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-RA-A741 
        5.85         3.39         3.72         5.75         4.80         3.88 
TCGA-UC-A7PF 
       93.99 

  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE 
                       137.16                        182.93 
  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE 
                        14.02                         12.82 
[1] "0.1 - 137.2 (14.0)" "0.0 - 182.9 (12.8)"
[1] "hr=" "1.4"
D32V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK  9(4Q35.2) MUTATED   34       10
  DEL PEAK  9(4Q35.2) WILD-TYPE 63       29
D32V3, multiclass
          clus
vv         DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  T1                                34                            63
  T2+T3+T4                          10                            29
[1] 2 2
[1] FALSE
D32V4, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.2) MUTATED   26 14
  DEL PEAK  9(4Q35.2) WILD-TYPE 61 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.2) MUTATED     26   14
  DEL PEAK  9(4Q35.2) WILD-TYPE   61   26
   clus
vv  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  0                          26                            61
  1                          14                            26
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  9(4Q35.2) MUTATED   30  0 15
  DEL PEAK  9(4Q35.2) WILD-TYPE 42  3 50
D32V5, multiclass
    clus
vv   DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  M0                          30                            42
  M1                           0                             3
  MX                          15                            50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(4Q35.2) MUTATED               0                               57
  DEL PEAK  9(4Q35.2) WILD-TYPE             2                               87
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK  9(4Q35.2) MUTATED                                               1
  DEL PEAK  9(4Q35.2) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK  9(4Q35.2) MUTATED                                     3
  DEL PEAK  9(4Q35.2) WILD-TYPE                                  17
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK  9(4Q35.2) MUTATED                                           2
  DEL PEAK  9(4Q35.2) WILD-TYPE                                         0
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK  9(4Q35.2) MUTATED                                              1
  DEL PEAK  9(4Q35.2) WILD-TYPE                                            3
D32V6, multiclass
                                               clus
vv                                              DEL PEAK  9(4Q35.2) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       57
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            1
                                               clus
vv                                              DEL PEAK  9(4Q35.2) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.2) MUTATED    9 55
  DEL PEAK  9(4Q35.2) WILD-TYPE 18 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.2) MUTATED      9   55
  DEL PEAK  9(4Q35.2) WILD-TYPE   18   94
     clus
vv    DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  NO                            9                            18
  YES                          55                            94
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4Q35.2) MUTATED                                  2     7
  DEL PEAK  9(4Q35.2) WILD-TYPE                                5     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(4Q35.2) MUTATED                           9
  DEL PEAK  9(4Q35.2) WILD-TYPE                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(4Q35.2) MUTATED                                           0    46
  DEL PEAK  9(4Q35.2) WILD-TYPE                                         1    84
D32V10, multiclass
                                           clus
vv                                          DEL PEAK  9(4Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              46
                                           clus
vv                                          DEL PEAK  9(4Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                 8
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                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"
D32V11, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.2) MUTATED    3 50
  DEL PEAK  9(4Q35.2) WILD-TYPE  8 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.2) MUTATED      3   50
  DEL PEAK  9(4Q35.2) WILD-TYPE    8   77
                        clus
vv                       DEL PEAK  9(4Q35.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       DEL PEAK  9(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            77
[1] 2 2
[1] FALSE
D32V12, continuous
D32V13, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.2) MUTATED   18  7
  DEL PEAK  9(4Q35.2) WILD-TYPE 30 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.2) MUTATED     18    7
  DEL PEAK  9(4Q35.2) WILD-TYPE   30   12
            clus
vv           DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  TUMOR FREE                          18                            30
  WITH TUMOR                           7                            12
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK  9(4Q35.2) MUTATED         1      5       2            50       6
  DEL PEAK  9(4Q35.2) WILD-TYPE       0      5       4            97       6
D32V14, multiclass
               clus
vv              DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  NIGERIA                                 1                             0
  RUSSIA                                  5                             5
  UKRAINE                                 2                             4
  UNITED STATES                          50                            97
  VIETNAM                                 6                             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                            G1 G2 G3 G4 GX
  DEL PEAK  9(4Q35.2) MUTATED    3 25 35  0  1
  DEL PEAK  9(4Q35.2) WILD-TYPE 11 58 37  1  4
D32V15, multiclass
    clus
vv   DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  G1                           3                            11
  G2                          25                            58
  G3                          35                            37
  G4                           0                             1
  GX                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V16, continuous
D32V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK  9(4Q35.2) MUTATED                                             4
  DEL PEAK  9(4Q35.2) WILD-TYPE                                          17
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK  9(4Q35.2) MUTATED                                        2
  DEL PEAK  9(4Q35.2) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK  9(4Q35.2) MUTATED                                                 1
  DEL PEAK  9(4Q35.2) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK  9(4Q35.2) MUTATED               15                  27
  DEL PEAK  9(4Q35.2) WILD-TYPE             21                  56
D32V18, multiclass
                                                 clus
vv                                                DEL PEAK  9(4Q35.2) 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                                                           15
  LIFELONG NON-SMOKER                                                      27
                                                 clus
vv                                                DEL PEAK  9(4Q35.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             21
  LIFELONG NON-SMOKER                                                        56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK  9(4Q35.2) MUTATED             6       15             3        4
  DEL PEAK  9(4Q35.2) WILD-TYPE          11       22             8        1
D32V20, multiclass
               clus
vv              DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  COMBINATION                             6                            11
  EXTERNAL                               15                            22
  EXTERNAL BEAM                           3                             8
  INTERNAL                                4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V21, binary
                               cls
clus                            0 1
  DEL PEAK  9(4Q35.2) MUTATED   6 2
  DEL PEAK  9(4Q35.2) WILD-TYPE 5 1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.2) MUTATED      6    2
  DEL PEAK  9(4Q35.2) WILD-TYPE    5    1
     clus
vv    DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  CGY                           6                             5
  GY                            2                             1
[1] 2 2
[1] FALSE
D32V22, continuous
D32V23, continuous
D32V24, continuous
D32V25, continuous
D32V26, continuous
D32V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  9(4Q35.2) MUTATED                                     0
  DEL PEAK  9(4Q35.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK  9(4Q35.2) MUTATED                                     3
  DEL PEAK  9(4Q35.2) WILD-TYPE                                   3
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK  9(4Q35.2) MUTATED                         2                       0
  DEL PEAK  9(4Q35.2) WILD-TYPE                       7                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK  9(4Q35.2) MUTATED                         1
  DEL PEAK  9(4Q35.2) WILD-TYPE                       4
D32V28, multiclass
                                     clus
vv                                    DEL PEAK  9(4Q35.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           3
  OTHER LOCATION, SPECIFY                                       2
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK  9(4Q35.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                         7
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK  9(4Q35.2) MUTATED                                               1
  DEL PEAK  9(4Q35.2) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK  9(4Q35.2) MUTATED                                                7
  DEL PEAK  9(4Q35.2) WILD-TYPE                                              3
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK  9(4Q35.2) MUTATED                                                                                  19
  DEL PEAK  9(4Q35.2) WILD-TYPE                                                                                35
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK  9(4Q35.2) MUTATED                                                                                             23
  DEL PEAK  9(4Q35.2) WILD-TYPE                                                                                           54
D32V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK  9(4Q35.2) 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)                                     19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          23
                                                                                              clus
vv                                                                                             DEL PEAK  9(4Q35.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       35
  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"
D32V30, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.2) MUTATED   16 22
  DEL PEAK  9(4Q35.2) WILD-TYPE 38 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.2) MUTATED     16   22
  DEL PEAK  9(4Q35.2) WILD-TYPE   38   37
         clus
vv        DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  ABSENT                           16                            38
  PRESENT                          22                            37
[1] 2 2
[1] FALSE
D32V31, continuous
D32V32, continuous
D32V33, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.2) MUTATED   17 30
  DEL PEAK  9(4Q35.2) WILD-TYPE 18 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.2) MUTATED     17   30
  DEL PEAK  9(4Q35.2) WILD-TYPE   18   51
                                          clus
vv                                         DEL PEAK  9(4Q35.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          30
                                          clus
vv                                         DEL PEAK  9(4Q35.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                18
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            51
[1] 2 2
[1] FALSE
D32V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK  9(4Q35.2) MUTATED       0                   40                   2
  DEL PEAK  9(4Q35.2) WILD-TYPE     3                   73                   3
D32V35, multiclass
                      clus
vv                     DEL PEAK  9(4Q35.2) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          40
  SIMPLE HYSTERECTOMY                            2
                      clus
vv                     DEL PEAK  9(4Q35.2) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            73
  SIMPLE HYSTERECTOMY                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK  9(4Q35.2) MUTATED              3          15         14
  DEL PEAK  9(4Q35.2) WILD-TYPE            5          25         26
D32V36, multiclass
              clus
vv             DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  CURRENT USER                           3                             5
  FORMER USER                           15                            25
  NEVER USED                            14                            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V37, continuous
D32V38, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.2) MUTATED   23  2
  DEL PEAK  9(4Q35.2) WILD-TYPE 50 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.2) MUTATED     23    2
  DEL PEAK  9(4Q35.2) WILD-TYPE   50   12
         clus
vv        DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  ABSENT                           23                            50
  PRESENT                           2                            12
[1] 2 2
[1] FALSE
D32V39, continuous
[1] "Remove cluster labels:"      "DEL PEAK  9(4Q35.2) MUTATED"
clus
  DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE 
                            2                             7 
                   TCGA-C5-A1MH                    TCGA-C5-A1MP 
"DEL PEAK  9(4Q35.2) WILD-TYPE" "DEL PEAK  9(4Q35.2) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-HM-A3JK 
"DEL PEAK  9(4Q35.2) WILD-TYPE" "DEL PEAK  9(4Q35.2) WILD-TYPE" 
                   TCGA-JW-A852                    TCGA-MU-A51Y 
"DEL PEAK  9(4Q35.2) WILD-TYPE" "DEL PEAK  9(4Q35.2) WILD-TYPE" 
                   TCGA-MU-A8JM 
"DEL PEAK  9(4Q35.2) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK  9(4Q35.2) MUTATED     1    0   9   20    4  2   2    2    1   3   0
  DEL PEAK  9(4Q35.2) WILD-TYPE   1    1  13   31   17  1   4    4    7  10   2
                               vv
clus                            T4 TX
  DEL PEAK  9(4Q35.2) MUTATED    0  2
  DEL PEAK  9(4Q35.2) WILD-TYPE  1  5
D32V40, multiclass
      clus
vv     DEL PEAK  9(4Q35.2) MUTATED DEL PEAK  9(4Q35.2) WILD-TYPE
  T1A                            1                             1
  T1A1                           0                             1
  T1B                            9                            13
  T1B1                          20                            31
  T1B2                           4                            17
  T2                             2                             1
  T2A                            2                             4
  T2A1                           2                             4
  T2A2                           1                             7
  T2B                            3                            10
  T3B                            0                             2
  T4                             0                             1
  TX                             2                             5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V41, continuous

Clustering(33) Variable = DEL PEAK 10(5Q22.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q22.3) MUTATED    34  11
  DEL PEAK 10(5Q22.3) WILD-TYPE 103  21
  DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE 
                           45                           124 
  DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE 
                           11                            21 
$`DEL PEAK 10(5Q22.3) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M6 
       11.44        68.84       144.16       177.04         5.46        31.40 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A3HD 
       30.21        35.01        38.99        35.61        40.93        52.01 
TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UE TCGA-DR-A0ZL TCGA-DS-A0VK 
       18.02        25.35        17.19        85.55        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 
        2.66       117.99         0.76        12.36         1.32         1.35 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2RJ 
       14.50        14.89        14.96        12.59         6.64         1.18 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY 
        2.24         0.10        20.35        23.84         0.92         0.66 
TCGA-FU-A3NI TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-JW-A5VI TCGA-JW-A69B 
        1.45         1.97        25.41        21.67        16.64        10.06 
TCGA-LP-A4AW TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.89         5.85         3.39 

$`DEL PEAK 10(5Q22.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BL 
       49.48        57.04        23.67        18.74        36.56       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MF 
       82.85        19.86        67.46        46.32        57.73        53.16 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        0.46         2.43         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-A3HF 
       83.05        78.35       100.14        38.43         0.82        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       73.41        60.69        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       58.88       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        8.28         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        1.48        13.91         0.69        14.99        13.58        13.48 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       45.96         0.53         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
        0.36        23.70         0.10         0.07         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70         4.47         6.12         1.22 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        2.17         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.35         1.32         1.12        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK 
       81.96        26.56        36.36        14.43        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
       15.58         5.13         0.10         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        3.72         3.45         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE 
                       177.04                        182.93 
  DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE 
                       14.960                        12.935 
[1] "0.1 - 177.0 (15.0)" "0.0 - 182.9 (12.9)"
[1] "hr=" "1.4"
D33V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK 10(5Q22.3) MUTATED   28        6
  DEL PEAK 10(5Q22.3) WILD-TYPE 69       33
D33V3, multiclass
          clus
vv         DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  T1                                28                            69
  T2+T3+T4                           6                            33
[1] 2 2
[1] FALSE
D33V4, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q22.3) MUTATED   20 11
  DEL PEAK 10(5Q22.3) WILD-TYPE 67 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q22.3) MUTATED     20   11
  DEL PEAK 10(5Q22.3) WILD-TYPE   67   29
   clus
vv  DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  0                          20                            67
  1                          11                            29
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 10(5Q22.3) MUTATED   17  0 18
  DEL PEAK 10(5Q22.3) WILD-TYPE 55  3 47
D33V5, multiclass
    clus
vv   DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  M0                          17                            55
  M1                           0                             3
  MX                          18                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(5Q22.3) MUTATED               0                               43
  DEL PEAK 10(5Q22.3) WILD-TYPE             2                              101
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 10(5Q22.3) MUTATED                                               0
  DEL PEAK 10(5Q22.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 10(5Q22.3) MUTATED                                     3
  DEL PEAK 10(5Q22.3) WILD-TYPE                                  17
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 10(5Q22.3) MUTATED                                           1
  DEL PEAK 10(5Q22.3) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 10(5Q22.3) MUTATED                                              0
  DEL PEAK 10(5Q22.3) WILD-TYPE                                            4
D33V6, multiclass
                                               clus
vv                                              DEL PEAK 10(5Q22.3) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       43
  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                                              DEL PEAK 10(5Q22.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        101
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 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"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q22.3) MUTATED    12  35
  DEL PEAK 10(5Q22.3) WILD-TYPE  15 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q22.3) MUTATED     12   35
  DEL PEAK 10(5Q22.3) WILD-TYPE   15  114
     clus
vv    DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  NO                           12                            15
  YES                          35                           114
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(5Q22.3) MUTATED                                  1     4
  DEL PEAK 10(5Q22.3) WILD-TYPE                                6    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(5Q22.3) MUTATED                           5
  DEL PEAK 10(5Q22.3) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(5Q22.3) MUTATED                                           0    37
  DEL PEAK 10(5Q22.3) WILD-TYPE                                         1    93
D33V10, multiclass
                                           clus
vv                                          DEL PEAK 10(5Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              37
                                           clus
vv                                          DEL PEAK 10(5Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                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"
D33V11, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q22.3) MUTATED    2 36
  DEL PEAK 10(5Q22.3) WILD-TYPE  9 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q22.3) MUTATED      2   36
  DEL PEAK 10(5Q22.3) WILD-TYPE    9   91
                        clus
vv                       DEL PEAK 10(5Q22.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          36
                        clus
vv                       DEL PEAK 10(5Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            91
[1] 2 2
[1] FALSE
D33V12, continuous
D33V13, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q22.3) MUTATED   12  9
  DEL PEAK 10(5Q22.3) WILD-TYPE 36 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q22.3) MUTATED     12    9
  DEL PEAK 10(5Q22.3) WILD-TYPE   36   10
            clus
vv           DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  TUMOR FREE                          12                            36
  WITH TUMOR                           9                            10
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 10(5Q22.3) MUTATED         0      5       0            39       3
  DEL PEAK 10(5Q22.3) WILD-TYPE       1      5       6           108       9
D33V14, multiclass
               clus
vv              DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 0                             6
  UNITED STATES                          39                           108
  VIETNAM                                 3                             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 10(5Q22.3) MUTATED    1 21 22  0  2
  DEL PEAK 10(5Q22.3) WILD-TYPE 13 62 50  1  3
D33V15, multiclass
    clus
vv   DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  G1                           1                            13
  G2                          21                            62
  G3                          22                            50
  G4                           0                             1
  GX                           2                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V16, continuous
D33V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 10(5Q22.3) MUTATED                                             4
  DEL PEAK 10(5Q22.3) WILD-TYPE                                          17
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 10(5Q22.3) MUTATED                                        2
  DEL PEAK 10(5Q22.3) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 10(5Q22.3) MUTATED                                                 0
  DEL PEAK 10(5Q22.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 10(5Q22.3) MUTATED               11                  21
  DEL PEAK 10(5Q22.3) WILD-TYPE             25                  62
D33V18, multiclass
                                                 clus
vv                                                DEL PEAK 10(5Q22.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           11
  LIFELONG NON-SMOKER                                                      21
                                                 clus
vv                                                DEL PEAK 10(5Q22.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             25
  LIFELONG NON-SMOKER                                                        62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 10(5Q22.3) MUTATED             7        5             5        0
  DEL PEAK 10(5Q22.3) WILD-TYPE          10       32             6        5
D33V20, multiclass
               clus
vv              DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  COMBINATION                             7                            10
  EXTERNAL                                5                            32
  EXTERNAL BEAM                           5                             6
  INTERNAL                                0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V21, binary
                               cls
clus                            0 1
  DEL PEAK 10(5Q22.3) MUTATED   3 0
  DEL PEAK 10(5Q22.3) WILD-TYPE 8 3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q22.3) MUTATED      3    0
  DEL PEAK 10(5Q22.3) WILD-TYPE    8    3
     clus
vv    DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  CGY                           3                             8
  GY                            0                             3
[1] 2 2
[1] FALSE
D33V22, continuous
D33V23, continuous
D33V24, continuous
D33V25, continuous
D33V26, continuous
D33V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 10(5Q22.3) MUTATED                                     0
  DEL PEAK 10(5Q22.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 10(5Q22.3) MUTATED                                     2
  DEL PEAK 10(5Q22.3) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 10(5Q22.3) MUTATED                         3                       0
  DEL PEAK 10(5Q22.3) WILD-TYPE                       6                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 10(5Q22.3) MUTATED                         1
  DEL PEAK 10(5Q22.3) WILD-TYPE                       4
D33V28, multiclass
                                     clus
vv                                    DEL PEAK 10(5Q22.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  OTHER LOCATION, SPECIFY                                       3
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK 10(5Q22.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                         6
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK 10(5Q22.3) MUTATED                                               1
  DEL PEAK 10(5Q22.3) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 10(5Q22.3) MUTATED                                                4
  DEL PEAK 10(5Q22.3) WILD-TYPE                                              6
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 10(5Q22.3) MUTATED                                                                                  15
  DEL PEAK 10(5Q22.3) WILD-TYPE                                                                                39
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 10(5Q22.3) MUTATED                                                                                             17
  DEL PEAK 10(5Q22.3) WILD-TYPE                                                                                           60
D33V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 10(5Q22.3) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          17
                                                                                              clus
vv                                                                                             DEL PEAK 10(5Q22.3) 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)                                       39
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V30, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q22.3) MUTATED   10 19
  DEL PEAK 10(5Q22.3) WILD-TYPE 44 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q22.3) MUTATED     10   19
  DEL PEAK 10(5Q22.3) WILD-TYPE   44   40
         clus
vv        DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  ABSENT                           10                            44
  PRESENT                          19                            40
[1] 2 2
[1] FALSE
D33V31, continuous
D33V32, continuous
D33V33, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q22.3) MUTATED    9 25
  DEL PEAK 10(5Q22.3) WILD-TYPE 26 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q22.3) MUTATED      9   25
  DEL PEAK 10(5Q22.3) WILD-TYPE   26   56
                                          clus
vv                                         DEL PEAK 10(5Q22.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          25
                                          clus
vv                                         DEL PEAK 10(5Q22.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            56
[1] 2 2
[1] FALSE
D33V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 10(5Q22.3) MUTATED       0                   33                   0
  DEL PEAK 10(5Q22.3) WILD-TYPE     3                   80                   5
D33V35, multiclass
                      clus
vv                     DEL PEAK 10(5Q22.3) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          33
  SIMPLE HYSTERECTOMY                            0
                      clus
vv                     DEL PEAK 10(5Q22.3) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            80
  SIMPLE HYSTERECTOMY                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 10(5Q22.3) MUTATED              1          12         11
  DEL PEAK 10(5Q22.3) WILD-TYPE            7          28         29
D33V36, multiclass
              clus
vv             DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  CURRENT USER                           1                             7
  FORMER USER                           12                            28
  NEVER USED                            11                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V37, continuous
D33V38, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q22.3) MUTATED   17  4
  DEL PEAK 10(5Q22.3) WILD-TYPE 56 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q22.3) MUTATED     17    4
  DEL PEAK 10(5Q22.3) WILD-TYPE   56   10
         clus
vv        DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  ABSENT                           17                            56
  PRESENT                           4                            10
[1] 2 2
[1] FALSE
D33V39, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 10(5Q22.3) MUTATED     1    0   6   15    6  0   1    2    0   2   1
  DEL PEAK 10(5Q22.3) WILD-TYPE   1    1  16   36   15  3   5    4    8  11   1
                               vv
clus                            T4 TX
  DEL PEAK 10(5Q22.3) MUTATED    0  2
  DEL PEAK 10(5Q22.3) WILD-TYPE  1  5
D33V40, multiclass
      clus
vv     DEL PEAK 10(5Q22.3) MUTATED DEL PEAK 10(5Q22.3) WILD-TYPE
  T1A                            1                             1
  T1A1                           0                             1
  T1B                            6                            16
  T1B1                          15                            36
  T1B2                           6                            15
  T2                             0                             3
  T2A                            1                             5
  T2A1                           2                             4
  T2A2                           0                             8
  T2B                            2                            11
  T3B                            1                             1
  T4                             0                             1
  TX                             2                             5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V41, continuous

Clustering(34) Variable = DEL PEAK 11(5Q35.2) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(5Q35.2) MUTATED    35  10
  DEL PEAK 11(5Q35.2) WILD-TYPE 102  22
  DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE 
                           45                           124 
  DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE 
                           10                            22 
$`DEL PEAK 11(5Q35.2) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 
       11.44       144.16       173.29         5.46        31.40        35.01 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7UC 
       38.99        35.61        40.93        18.02        25.35        17.19 
TCGA-C5-A7UE TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QS 
       85.55        87.75        36.76         2.66       117.99         0.76 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 
       12.36         1.32        14.50         1.35        14.50        14.89 
TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM 
       14.96        12.59         6.64         0.03         1.18         2.24 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A40J 
        0.10        20.35        23.84         0.92         0.66         1.35 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-JW-A5VI TCGA-LP-A4AW 
        1.97        25.41        21.67       137.16        16.64         0.89 
TCGA-LP-A5U3 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.82         5.85         3.39 

$`DEL PEAK 11(5Q35.2) 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-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      177.04        82.85        19.86        67.46        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       57.73        53.16         0.46         2.43         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
        0.82        52.01        17.85        20.42       182.93       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7UI 
      134.33        15.48         9.67        73.41        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ 
        9.34        13.61         2.73        58.88       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HS 
       16.83        16.18         7.33         8.28         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S 
        0.62        13.05         1.18         1.35         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26         1.48        13.91         0.69        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       13.58        13.48        45.96         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        4.04         0.36        23.70         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        1.22         2.17         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A3JK TCGA-HM-A4S6 
        0.82         3.52         1.32         1.12        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
        4.11       147.39        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK 
       81.96        26.56        36.36        14.43        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MU-A51Y 
       15.58        10.06         5.13         0.10         0.07        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-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        3.72         3.45         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE 
                       173.29                        182.93 
  DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE 
                       14.500                        13.265 
[1] "0.0 - 173.3 (14.5)" "0.0 - 182.9 (13.3)"
[1] "hr=" "1.2"
D34V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK 11(5Q35.2) MUTATED   28        7
  DEL PEAK 11(5Q35.2) WILD-TYPE 69       32
D34V3, multiclass
          clus
vv         DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  T1                                28                            69
  T2+T3+T4                           7                            32
[1] 2 2
[1] FALSE
D34V4, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q35.2) MUTATED   22 11
  DEL PEAK 11(5Q35.2) WILD-TYPE 65 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.2) MUTATED     22   11
  DEL PEAK 11(5Q35.2) WILD-TYPE   65   29
   clus
vv  DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  0                          22                            65
  1                          11                            29
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 11(5Q35.2) MUTATED   21  0 15
  DEL PEAK 11(5Q35.2) WILD-TYPE 51  3 50
D34V5, multiclass
    clus
vv   DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  M0                          21                            51
  M1                           0                             3
  MX                          15                            50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(5Q35.2) MUTATED               0                               42
  DEL PEAK 11(5Q35.2) WILD-TYPE             2                              102
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 11(5Q35.2) MUTATED                                               0
  DEL PEAK 11(5Q35.2) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 11(5Q35.2) MUTATED                                     3
  DEL PEAK 11(5Q35.2) WILD-TYPE                                  17
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 11(5Q35.2) MUTATED                                           2
  DEL PEAK 11(5Q35.2) WILD-TYPE                                         0
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 11(5Q35.2) MUTATED                                              0
  DEL PEAK 11(5Q35.2) WILD-TYPE                                            4
D34V6, multiclass
                                               clus
vv                                              DEL PEAK 11(5Q35.2) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       42
  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                                              DEL PEAK 11(5Q35.2) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        102
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q35.2) MUTATED    11  36
  DEL PEAK 11(5Q35.2) WILD-TYPE  16 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.2) MUTATED     11   36
  DEL PEAK 11(5Q35.2) WILD-TYPE   16  113
     clus
vv    DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  NO                           11                            16
  YES                          36                           113
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(5Q35.2) MUTATED                                  2     5
  DEL PEAK 11(5Q35.2) WILD-TYPE                                5    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(5Q35.2) MUTATED                           4
  DEL PEAK 11(5Q35.2) WILD-TYPE                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(5Q35.2) MUTATED                                           0    36
  DEL PEAK 11(5Q35.2) WILD-TYPE                                         1    94
D34V10, multiclass
                                           clus
vv                                          DEL PEAK 11(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              36
                                           clus
vv                                          DEL PEAK 11(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      5
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                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"
D34V11, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q35.2) MUTATED    1 37
  DEL PEAK 11(5Q35.2) WILD-TYPE 10 90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.2) MUTATED      1   37
  DEL PEAK 11(5Q35.2) WILD-TYPE   10   90
                        clus
vv                       DEL PEAK 11(5Q35.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       DEL PEAK 11(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                            90
[1] 2 2
[1] FALSE
D34V12, continuous
D34V13, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q35.2) MUTATED   12  8
  DEL PEAK 11(5Q35.2) WILD-TYPE 36 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.2) MUTATED     12    8
  DEL PEAK 11(5Q35.2) WILD-TYPE   36   11
            clus
vv           DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  TUMOR FREE                          12                            36
  WITH TUMOR                           8                            11
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 11(5Q35.2) MUTATED         0      5       1            37       4
  DEL PEAK 11(5Q35.2) WILD-TYPE       1      5       5           110       8
D34V14, multiclass
               clus
vv              DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  5                             5
  UKRAINE                                 1                             5
  UNITED STATES                          37                           110
  VIETNAM                                 4                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 11(5Q35.2) MUTATED    1 18 26  0  1
  DEL PEAK 11(5Q35.2) WILD-TYPE 13 65 46  1  4
D34V15, multiclass
    clus
vv   DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  G1                           1                            13
  G2                          18                            65
  G3                          26                            46
  G4                           0                             1
  GX                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V16, continuous
D34V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 11(5Q35.2) MUTATED                                             4
  DEL PEAK 11(5Q35.2) WILD-TYPE                                          17
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 11(5Q35.2) MUTATED                                        1
  DEL PEAK 11(5Q35.2) WILD-TYPE                                      7
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 11(5Q35.2) MUTATED                                                 0
  DEL PEAK 11(5Q35.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 11(5Q35.2) MUTATED               10                  22
  DEL PEAK 11(5Q35.2) WILD-TYPE             26                  61
D34V18, multiclass
                                                 clus
vv                                                DEL PEAK 11(5Q35.2) 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                                                      22
                                                 clus
vv                                                DEL PEAK 11(5Q35.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             26
  LIFELONG NON-SMOKER                                                        61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 11(5Q35.2) MUTATED             7        7             4        0
  DEL PEAK 11(5Q35.2) WILD-TYPE          10       30             7        5
D34V20, multiclass
               clus
vv              DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  COMBINATION                             7                            10
  EXTERNAL                                7                            30
  EXTERNAL BEAM                           4                             7
  INTERNAL                                0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V21, binary
                               cls
clus                            0 1
  DEL PEAK 11(5Q35.2) MUTATED   3 0
  DEL PEAK 11(5Q35.2) WILD-TYPE 8 3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.2) MUTATED      3    0
  DEL PEAK 11(5Q35.2) WILD-TYPE    8    3
     clus
vv    DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  CGY                           3                             8
  GY                            0                             3
[1] 2 2
[1] FALSE
D34V22, continuous
D34V23, continuous
D34V24, continuous
D34V25, continuous
D34V26, continuous
D34V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 11(5Q35.2) MUTATED                                     0
  DEL PEAK 11(5Q35.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 11(5Q35.2) MUTATED                                     2
  DEL PEAK 11(5Q35.2) WILD-TYPE                                   4
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 11(5Q35.2) MUTATED                         2                       0
  DEL PEAK 11(5Q35.2) WILD-TYPE                       7                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 11(5Q35.2) MUTATED                         1
  DEL PEAK 11(5Q35.2) WILD-TYPE                       4
D34V28, multiclass
                                     clus
vv                                    DEL PEAK 11(5Q35.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  OTHER LOCATION, SPECIFY                                       2
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK 11(5Q35.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             4
  OTHER LOCATION, SPECIFY                                         7
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK 11(5Q35.2) MUTATED                                               0
  DEL PEAK 11(5Q35.2) WILD-TYPE                                             2
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 11(5Q35.2) MUTATED                                                4
  DEL PEAK 11(5Q35.2) WILD-TYPE                                              6
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 11(5Q35.2) MUTATED                                                                                  16
  DEL PEAK 11(5Q35.2) WILD-TYPE                                                                                38
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 11(5Q35.2) MUTATED                                                                                             18
  DEL PEAK 11(5Q35.2) WILD-TYPE                                                                                           59
D34V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 11(5Q35.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                          0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                         4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                     16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          18
                                                                                              clus
vv                                                                                             DEL PEAK 11(5Q35.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            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"
D34V30, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q35.2) MUTATED   12 19
  DEL PEAK 11(5Q35.2) WILD-TYPE 42 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.2) MUTATED     12   19
  DEL PEAK 11(5Q35.2) WILD-TYPE   42   40
         clus
vv        DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  ABSENT                           12                            42
  PRESENT                          19                            40
[1] 2 2
[1] FALSE
D34V31, continuous
D34V32, continuous
D34V33, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q35.2) MUTATED    7 28
  DEL PEAK 11(5Q35.2) WILD-TYPE 28 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.2) MUTATED      7   28
  DEL PEAK 11(5Q35.2) WILD-TYPE   28   53
                                          clus
vv                                         DEL PEAK 11(5Q35.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               7
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          28
                                          clus
vv                                         DEL PEAK 11(5Q35.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            53
[1] 2 2
[1] FALSE
D34V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 11(5Q35.2) MUTATED       0                   32                   2
  DEL PEAK 11(5Q35.2) WILD-TYPE     3                   81                   3
D34V35, multiclass
                      clus
vv                     DEL PEAK 11(5Q35.2) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          32
  SIMPLE HYSTERECTOMY                            2
                      clus
vv                     DEL PEAK 11(5Q35.2) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            81
  SIMPLE HYSTERECTOMY                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 11(5Q35.2) MUTATED              1          11         12
  DEL PEAK 11(5Q35.2) WILD-TYPE            7          29         28
D34V36, multiclass
              clus
vv             DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  CURRENT USER                           1                             7
  FORMER USER                           11                            29
  NEVER USED                            12                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V37, continuous
D34V38, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q35.2) MUTATED   20  3
  DEL PEAK 11(5Q35.2) WILD-TYPE 53 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.2) MUTATED     20    3
  DEL PEAK 11(5Q35.2) WILD-TYPE   53   11
         clus
vv        DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  ABSENT                           20                            53
  PRESENT                           3                            11
[1] 2 2
[1] FALSE
D34V39, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 11(5Q35.2) MUTATED     2    0   5   16    5  0   1    3    0   2   1
  DEL PEAK 11(5Q35.2) WILD-TYPE   0    1  17   35   16  3   5    3    8  11   1
                               vv
clus                            T4 TX
  DEL PEAK 11(5Q35.2) MUTATED    0  2
  DEL PEAK 11(5Q35.2) WILD-TYPE  1  5
D34V40, multiclass
      clus
vv     DEL PEAK 11(5Q35.2) MUTATED DEL PEAK 11(5Q35.2) WILD-TYPE
  T1A                            2                             0
  T1A1                           0                             1
  T1B                            5                            17
  T1B1                          16                            35
  T1B2                           5                            16
  T2                             0                             3
  T2A                            1                             5
  T2A1                           3                             3
  T2A2                           0                             8
  T2B                            2                            11
  T3B                            1                             1
  T4                             0                             1
  TX                             2                             5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V41, continuous

Clustering(35) Variable = DEL PEAK 12(6P24.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6P24.2) MUTATED    19   3
  DEL PEAK 12(6P24.2) WILD-TYPE 118  29
  DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE 
                           22                           147 
  DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE 
                            3                            29 
$`DEL PEAK 12(6P24.2) MUTATED`
TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7CO TCGA-C5-A7X3 
       19.86        30.21        73.18       182.93        73.41         9.34 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A556 
       36.76       117.99        22.98         1.18        12.66        14.89 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2RC TCGA-EK-A2RN TCGA-EX-A1H6 TCGA-FU-A3HY 
       14.96        13.58         4.04         0.10         7.92         0.66 
TCGA-HG-A2PA TCGA-IR-A3L7 TCGA-JW-A5VJ TCGA-UC-A7PF 
       25.41       147.39        19.33        93.99 

$`DEL PEAK 12(6P24.2) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       38.99        35.61         0.46         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
        0.82        52.01        18.02        17.85        20.42        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48         9.67        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       60.69        94.95        13.61         2.73        87.75        58.88 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
        2.66       118.65        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       13.05        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26         1.48        13.91         0.69        14.99 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         0.03         0.36         1.18        23.70         2.24 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 
        0.07         0.10         0.10         0.03        20.35         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-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-HM-A3JJ 
        3.52         1.35         1.32         1.97         1.12        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93         4.11       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU 
       16.64        20.48        15.58        10.06         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        5.85         3.39         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       19.59         3.88        11.67 

  DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE 
                       182.93                        177.04 
  DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE 
                       19.595                        12.590 
[1] "0.1 - 182.9 (19.6)" "0.0 - 177.0 (12.6)"
[1] "hr=" "2.2"
D35V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK 12(6P24.2) MUTATED   14        4
  DEL PEAK 12(6P24.2) WILD-TYPE 83       35
D35V3, multiclass
          clus
vv         DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  T1                                14                            83
  T2+T3+T4                           4                            35
[1] 2 2
[1] FALSE
D35V4, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P24.2) MUTATED    8  8
  DEL PEAK 12(6P24.2) WILD-TYPE 79 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P24.2) MUTATED      8    8
  DEL PEAK 12(6P24.2) WILD-TYPE   79   32
   clus
vv  DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  0                           8                            79
  1                           8                            32
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 12(6P24.2) MUTATED   12  0  6
  DEL PEAK 12(6P24.2) WILD-TYPE 60  3 59
D35V5, multiclass
    clus
vv   DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  M0                          12                            60
  M1                           0                             3
  MX                           6                            59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(6P24.2) MUTATED               0                               21
  DEL PEAK 12(6P24.2) WILD-TYPE             2                              123
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 12(6P24.2) MUTATED                                               0
  DEL PEAK 12(6P24.2) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 12(6P24.2) MUTATED                                     1
  DEL PEAK 12(6P24.2) WILD-TYPE                                  19
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 12(6P24.2) MUTATED                                           1
  DEL PEAK 12(6P24.2) WILD-TYPE                                         1
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 12(6P24.2) MUTATED                                              0
  DEL PEAK 12(6P24.2) WILD-TYPE                                            4
D35V6, multiclass
                                               clus
vv                                              DEL PEAK 12(6P24.2) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       21
  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                                              DEL PEAK 12(6P24.2) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 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"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(6P24.2) MUTATED     3  20
  DEL PEAK 12(6P24.2) WILD-TYPE  24 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P24.2) MUTATED      3   20
  DEL PEAK 12(6P24.2) WILD-TYPE   24  129
     clus
vv    DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  NO                            3                            24
  YES                          20                           129
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6P24.2) MUTATED                                  1     2
  DEL PEAK 12(6P24.2) WILD-TYPE                                6    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(6P24.2) MUTATED                           0
  DEL PEAK 12(6P24.2) WILD-TYPE                        18
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(6P24.2) MUTATED                                           0    17
  DEL PEAK 12(6P24.2) WILD-TYPE                                         1   113
D35V10, multiclass
                                           clus
vv                                          DEL PEAK 12(6P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              17
                                           clus
vv                                          DEL PEAK 12(6P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      6
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                               cls
clus                              0   1
  DEL PEAK 12(6P24.2) MUTATED     1  15
  DEL PEAK 12(6P24.2) WILD-TYPE  10 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P24.2) MUTATED      1   15
  DEL PEAK 12(6P24.2) WILD-TYPE   10  112
                        clus
vv                       DEL PEAK 12(6P24.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK 12(6P24.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           112
[1] 2 2
[1] FALSE
D35V12, continuous
D35V13, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P24.2) MUTATED    7  2
  DEL PEAK 12(6P24.2) WILD-TYPE 41 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P24.2) MUTATED      7    2
  DEL PEAK 12(6P24.2) WILD-TYPE   41   17
            clus
vv           DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  TUMOR FREE                           7                            41
  WITH TUMOR                           2                            17
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 12(6P24.2) MUTATED         0      2       1            18       2
  DEL PEAK 12(6P24.2) WILD-TYPE       1      8       5           129      10
D35V14, multiclass
               clus
vv              DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  2                             8
  UKRAINE                                 1                             5
  UNITED STATES                          18                           129
  VIETNAM                                 2                            10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 12(6P24.2) MUTATED    1 13  9  0  0
  DEL PEAK 12(6P24.2) WILD-TYPE 13 70 63  1  5
D35V15, multiclass
    clus
vv   DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  G1                           1                            13
  G2                          13                            70
  G3                           9                            63
  G4                           0                             1
  GX                           0                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V16, continuous
D35V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 12(6P24.2) MUTATED                                             3
  DEL PEAK 12(6P24.2) WILD-TYPE                                          18
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 12(6P24.2) MUTATED                                        2
  DEL PEAK 12(6P24.2) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 12(6P24.2) MUTATED                                                 0
  DEL PEAK 12(6P24.2) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 12(6P24.2) MUTATED                5                  10
  DEL PEAK 12(6P24.2) WILD-TYPE             31                  73
D35V18, multiclass
                                                 clus
vv                                                DEL PEAK 12(6P24.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                            5
  LIFELONG NON-SMOKER                                                      10
                                                 clus
vv                                                DEL PEAK 12(6P24.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             31
  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"
D35V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 12(6P24.2) MUTATED             0        4             4        1
  DEL PEAK 12(6P24.2) WILD-TYPE          17       33             7        4
D35V20, multiclass
               clus
vv              DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  COMBINATION                             0                            17
  EXTERNAL                                4                            33
  EXTERNAL BEAM                           4                             7
  INTERNAL                                1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V21, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P24.2) MUTATED    1  0
  DEL PEAK 12(6P24.2) WILD-TYPE 10  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P24.2) MUTATED      1    0
  DEL PEAK 12(6P24.2) WILD-TYPE   10    3
     clus
vv    DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  CGY                           1                            10
  GY                            0                             3
[1] 2 2
[1] FALSE
D35V22, continuous
D35V23, continuous
D35V24, continuous
D35V25, continuous
D35V26, continuous
D35V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 12(6P24.2) MUTATED                                     0
  DEL PEAK 12(6P24.2) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 12(6P24.2) MUTATED                                     0
  DEL PEAK 12(6P24.2) WILD-TYPE                                   6
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 12(6P24.2) MUTATED                         3                       0
  DEL PEAK 12(6P24.2) WILD-TYPE                       6                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 12(6P24.2) MUTATED                         1
  DEL PEAK 12(6P24.2) WILD-TYPE                       4
D35V28, multiclass
                                     clus
vv                                    DEL PEAK 12(6P24.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  OTHER LOCATION, SPECIFY                                       3
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       1
                                     clus
vv                                    DEL PEAK 12(6P24.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             6
  OTHER LOCATION, SPECIFY                                         6
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK 12(6P24.2) MUTATED                                               1
  DEL PEAK 12(6P24.2) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 12(6P24.2) MUTATED                                                2
  DEL PEAK 12(6P24.2) WILD-TYPE                                              8
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 12(6P24.2) MUTATED                                                                                   5
  DEL PEAK 12(6P24.2) WILD-TYPE                                                                                49
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 12(6P24.2) MUTATED                                                                                             11
  DEL PEAK 12(6P24.2) WILD-TYPE                                                                                           66
D35V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 12(6P24.2) 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)                                      5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          11
                                                                                              clus
vv                                                                                             DEL PEAK 12(6P24.2) 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)                                       49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V30, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P24.2) MUTATED    5 11
  DEL PEAK 12(6P24.2) WILD-TYPE 49 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P24.2) MUTATED      5   11
  DEL PEAK 12(6P24.2) WILD-TYPE   49   48
         clus
vv        DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  ABSENT                            5                            49
  PRESENT                          11                            48
[1] 2 2
[1] FALSE
D35V31, continuous
D35V32, continuous
D35V33, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P24.2) MUTATED    5 10
  DEL PEAK 12(6P24.2) WILD-TYPE 30 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P24.2) MUTATED      5   10
  DEL PEAK 12(6P24.2) WILD-TYPE   30   71
                                          clus
vv                                         DEL PEAK 12(6P24.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          10
                                          clus
vv                                         DEL PEAK 12(6P24.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            71
[1] 2 2
[1] FALSE
D35V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 12(6P24.2) MUTATED       0                   17                   0
  DEL PEAK 12(6P24.2) WILD-TYPE     3                   96                   5
D35V35, multiclass
                      clus
vv                     DEL PEAK 12(6P24.2) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          17
  SIMPLE HYSTERECTOMY                            0
                      clus
vv                     DEL PEAK 12(6P24.2) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            96
  SIMPLE HYSTERECTOMY                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 12(6P24.2) MUTATED              2           5          8
  DEL PEAK 12(6P24.2) WILD-TYPE            6          35         32
D35V36, multiclass
              clus
vv             DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  CURRENT USER                           2                             6
  FORMER USER                            5                            35
  NEVER USED                             8                            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V37, continuous
D35V38, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P24.2) MUTATED   11  2
  DEL PEAK 12(6P24.2) WILD-TYPE 62 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P24.2) MUTATED     11    2
  DEL PEAK 12(6P24.2) WILD-TYPE   62   12
         clus
vv        DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  ABSENT                           11                            62
  PRESENT                           2                            12
[1] 2 2
[1] FALSE
D35V39, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 12(6P24.2) MUTATED     0    0   4    8    2  0   0    0    1   2   1
  DEL PEAK 12(6P24.2) WILD-TYPE   2    1  18   43   19  3   6    6    7  11   1
                               vv
clus                            T4 TX
  DEL PEAK 12(6P24.2) MUTATED    0  0
  DEL PEAK 12(6P24.2) WILD-TYPE  1  7
D35V40, multiclass
      clus
vv     DEL PEAK 12(6P24.2) MUTATED DEL PEAK 12(6P24.2) WILD-TYPE
  T1A                            0                             2
  T1A1                           0                             1
  T1B                            4                            18
  T1B1                           8                            43
  T1B2                           2                            19
  T2                             0                             3
  T2A                            0                             6
  T2A1                           0                             6
  T2A2                           1                             7
  T2B                            2                            11
  T3B                            1                             1
  T4                             0                             1
  TX                             0                             7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V41, continuous

Clustering(36) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 13(6Q26) MUTATED   47  8
  DEL PEAK 13(6Q26) WILD-TYPE 90 24
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         55                         114 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                          8                          24 
$`DEL PEAK 13(6Q26) MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 
       49.48        23.67        36.56       173.29        82.85        67.46 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LZ 
       30.21        35.01        57.73        73.18        73.45       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CO 
       38.43        52.01        17.85       182.93        25.35        73.41 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DS-A0VM TCGA-EA-A1QT TCGA-EA-A3QE 
       60.69        94.95         9.34       117.99        12.36         1.18 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX 
       14.50         1.81        12.66        14.89        14.96        13.58 
TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RM TCGA-EK-A2RN 
       12.59         0.53         0.07         4.04         2.24         0.10 
TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A449 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3YQ 
        0.10         7.92        14.70        23.84         0.66         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH 
        1.35         1.32        20.78       147.39       117.40        78.71 
TCGA-JW-A5VJ TCGA-LP-A4AX TCGA-MU-A5YI TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V 
       19.33         0.07         0.03         3.45         3.39        19.59 
TCGA-UC-A7PD 
       11.67 

$`DEL PEAK 13(6Q26) 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-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH 
        5.46        19.86        31.40        46.32        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       35.61         0.46         2.43        40.93         3.58        44.22 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CJ 
       83.05        78.35         0.82        18.02        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X5 
      134.33        15.48         9.67        17.19        85.55        13.61 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN 
        2.73        87.75        58.88        36.76         2.66       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 
        1.74         1.32         0.82         0.62        13.05        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35         1.35        12.82         0.26         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 
        0.69        14.99        13.48        45.96         6.64         0.59 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK 
        0.03         0.36         1.18        23.70         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        0.03        20.35         6.94         4.47         6.12         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 
        0.82         1.97         1.12        25.41        21.67        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
        4.11       137.16        66.81        96.95        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        14.43        16.64        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM 
        5.13         0.10         0.89         0.82        13.87         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       29.72         0.07         4.34         2.96         3.72         5.85 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PF 
        3.72         5.75         4.80         6.25         3.88        93.99 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       0.03                        0.03 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     182.93                      177.04 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     17.850                       9.865 
[1] "0.0 - 182.9 (17.9)" "0.0 - 177.0 (9.9)" 
[1] "hr=" "2.1"
D36V2, continuous
                             vv
clus                          T1 T2+T3+T4
  DEL PEAK 13(6Q26) MUTATED   31       11
  DEL PEAK 13(6Q26) WILD-TYPE 66       28
D36V3, multiclass
          clus
vv         DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  T1                              31                          66
  T2+T3+T4                        11                          28
[1] 2 2
[1] FALSE
D36V4, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   25 13
  DEL PEAK 13(6Q26) WILD-TYPE 62 27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     25   13
  DEL PEAK 13(6Q26) WILD-TYPE   62   27
   clus
vv  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  0                        25                          62
  1                        13                          27
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK 13(6Q26) MUTATED   23  1 19
  DEL PEAK 13(6Q26) WILD-TYPE 49  2 46
D36V5, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  M0                        23                          49
  M1                         1                           2
  MX                        19                          46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(6Q26) MUTATED               0                               51
  DEL PEAK 13(6Q26) WILD-TYPE             2                               93
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 13(6Q26) MUTATED                                               0
  DEL PEAK 13(6Q26) WILD-TYPE                                             4
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                     8
  DEL PEAK 13(6Q26) WILD-TYPE                                  12
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 13(6Q26) MUTATED                                           1
  DEL PEAK 13(6Q26) WILD-TYPE                                         1
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 13(6Q26) MUTATED                                              1
  DEL PEAK 13(6Q26) WILD-TYPE                                            3
D36V6, multiclass
                                               clus
vv                                              DEL PEAK 13(6Q26) MUTATED
  ADENOSQUAMOUS                                                         0
  CERVICAL SQUAMOUS CELL CARCINOMA                                     51
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                         0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                   8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                             1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                          1
                                               clus
vv                                              DEL PEAK 13(6Q26) WILD-TYPE
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                       93
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    12
  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"
D36V7, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED    8 53
  DEL PEAK 13(6Q26) WILD-TYPE 19 96
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED      8   53
  DEL PEAK 13(6Q26) WILD-TYPE   19   96
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                          8                          19
  YES                        53                          96
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6Q26) MUTATED                                  2     4
  DEL PEAK 13(6Q26) WILD-TYPE                                5    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(6Q26) MUTATED                           7
  DEL PEAK 13(6Q26) WILD-TYPE                        11
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(6Q26) MUTATED                                           1    46
  DEL PEAK 13(6Q26) WILD-TYPE                                         0    84
D36V10, multiclass
                                           clus
vv                                          DEL PEAK 13(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             4
  BLACK OR AFRICAN AMERICAN                                         7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            46
                                           clus
vv                                          DEL PEAK 13(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    5
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              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"
D36V11, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED    2 45
  DEL PEAK 13(6Q26) WILD-TYPE  9 82
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED      2   45
  DEL PEAK 13(6Q26) WILD-TYPE    9   82
                        clus
vv                       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                           9
  NOT HISPANIC OR LATINO                        45                          82
[1] 2 2
[1] FALSE
D36V12, continuous
D36V13, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   20  6
  DEL PEAK 13(6Q26) WILD-TYPE 28 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     20    6
  DEL PEAK 13(6Q26) WILD-TYPE   28   13
            clus
vv           DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  TUMOR FREE                        20                          28
  WITH TUMOR                         6                          13
[1] 2 2
[1] FALSE
                             vv
clus                          NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 13(6Q26) MUTATED         0      3       2            52       4
  DEL PEAK 13(6Q26) WILD-TYPE       1      7       4            95       8
D36V14, multiclass
               clus
vv              DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NIGERIA                               0                           1
  RUSSIA                                3                           7
  UKRAINE                               2                           4
  UNITED STATES                        52                          95
  VIETNAM                               4                           8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  DEL PEAK 13(6Q26) MUTATED    4 26 28  1  1
  DEL PEAK 13(6Q26) WILD-TYPE 10 57 44  0  4
D36V15, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  G1                         4                          10
  G2                        26                          57
  G3                        28                          44
  G4                         1                           0
  GX                         1                           4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V16, continuous
D36V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 13(6Q26) MUTATED                                             8
  DEL PEAK 13(6Q26) WILD-TYPE                                          13
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 13(6Q26) MUTATED                                        2
  DEL PEAK 13(6Q26) WILD-TYPE                                      6
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 13(6Q26) MUTATED                                                 0
  DEL PEAK 13(6Q26) WILD-TYPE                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 13(6Q26) MUTATED               11                  27
  DEL PEAK 13(6Q26) WILD-TYPE             25                  56
D36V18, multiclass
                                                 clus
vv                                                DEL PEAK 13(6Q26) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                  2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                         0
  CURRENT SMOKER                                                         11
  LIFELONG NON-SMOKER                                                    27
                                                 clus
vv                                                DEL PEAK 13(6Q26) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           25
  LIFELONG NON-SMOKER                                                      56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V19, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 13(6Q26) MUTATED             5       10             4        3
  DEL PEAK 13(6Q26) WILD-TYPE          12       27             7        2
D36V20, multiclass
               clus
vv              DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  COMBINATION                           5                          12
  EXTERNAL                             10                          27
  EXTERNAL BEAM                         4                           7
  INTERNAL                              3                           2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V21, binary
                             cls
clus                          0 1
  DEL PEAK 13(6Q26) MUTATED   3 1
  DEL PEAK 13(6Q26) WILD-TYPE 8 2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED      3    1
  DEL PEAK 13(6Q26) WILD-TYPE    8    2
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  CGY                         3                           8
  GY                          1                           2
[1] 2 2
[1] FALSE
D36V22, continuous
D36V23, continuous
D36V24, continuous
D36V25, continuous
D36V26, continuous
D36V27, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 13(6Q26) MUTATED                                     1
  DEL PEAK 13(6Q26) WILD-TYPE                                   1
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 13(6Q26) MUTATED                                     1
  DEL PEAK 13(6Q26) WILD-TYPE                                   5
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 13(6Q26) MUTATED                         3                       0
  DEL PEAK 13(6Q26) WILD-TYPE                       6                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  DEL PEAK 13(6Q26) MUTATED                         2
  DEL PEAK 13(6Q26) WILD-TYPE                       3
D36V28, multiclass
                                     clus
vv                                    DEL PEAK 13(6Q26) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         1
  OTHER LOCATION, SPECIFY                                     3
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     2
                                     clus
vv                                    DEL PEAK 13(6Q26) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           5
  OTHER LOCATION, SPECIFY                                       6
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       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)
  DEL PEAK 13(6Q26) MUTATED                                               2
  DEL PEAK 13(6Q26) WILD-TYPE                                             0
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 13(6Q26) MUTATED                                                4
  DEL PEAK 13(6Q26) WILD-TYPE                                              6
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 13(6Q26) MUTATED                                                                                  18
  DEL PEAK 13(6Q26) WILD-TYPE                                                                                36
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 13(6Q26) MUTATED                                                                                             23
  DEL PEAK 13(6Q26) WILD-TYPE                                                                                           54
D36V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 13(6Q26) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       4
  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)                        23
                                                                                              clus
vv                                                                                             DEL PEAK 13(6Q26) WILD-TYPE
  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)                                     36
  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"
D36V30, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   17 20
  DEL PEAK 13(6Q26) WILD-TYPE 37 39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     17   20
  DEL PEAK 13(6Q26) WILD-TYPE   37   39
         clus
vv        DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  ABSENT                         17                          37
  PRESENT                        20                          39
[1] 2 2
[1] FALSE
D36V31, continuous
D36V32, continuous
D36V33, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   10 26
  DEL PEAK 13(6Q26) WILD-TYPE 25 55
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     10   26
  DEL PEAK 13(6Q26) WILD-TYPE   25   55
                                          clus
vv                                         DEL PEAK 13(6Q26) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            10
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        26
                                          clus
vv                                         DEL PEAK 13(6Q26) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          55
[1] 2 2
[1] FALSE
D36V34, continuous
                             vv
clus                          OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 13(6Q26) MUTATED       1                   39                   1
  DEL PEAK 13(6Q26) WILD-TYPE     2                   74                   4
D36V35, multiclass
                      clus
vv                     DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  OTHER                                        1                           2
  RADICAL HYSTERECTOMY                        39                          74
  SIMPLE HYSTERECTOMY                          1                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  DEL PEAK 13(6Q26) MUTATED              3          15         12
  DEL PEAK 13(6Q26) WILD-TYPE            5          25         28
D36V36, multiclass
              clus
vv             DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  CURRENT USER                         3                           5
  FORMER USER                         15                          25
  NEVER USED                          12                          28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V37, continuous
D36V38, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   25  5
  DEL PEAK 13(6Q26) WILD-TYPE 48  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     25    5
  DEL PEAK 13(6Q26) WILD-TYPE   48    9
         clus
vv        DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  ABSENT                         25                          48
  PRESENT                         5                           9
[1] 2 2
[1] FALSE
D36V39, continuous
[1] "Remove cluster labels:"    "DEL PEAK 13(6Q26) MUTATED"
clus
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                          1                           8 
                 TCGA-C5-A1BN                  TCGA-C5-A1MH 
"DEL PEAK 13(6Q26) WILD-TYPE" "DEL PEAK 13(6Q26) WILD-TYPE" 
                 TCGA-C5-A1MN                  TCGA-C5-A1MP 
"DEL PEAK 13(6Q26) WILD-TYPE" "DEL PEAK 13(6Q26) WILD-TYPE" 
                 TCGA-EK-A2RO                  TCGA-JW-A852 
"DEL PEAK 13(6Q26) WILD-TYPE" "DEL PEAK 13(6Q26) WILD-TYPE" 
                 TCGA-MU-A51Y                  TCGA-MU-A8JM 
"DEL PEAK 13(6Q26) WILD-TYPE" "DEL PEAK 13(6Q26) WILD-TYPE" 
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 13(6Q26) MUTATED     0    1  11   17    2  1   0    4    1   4   1
  DEL PEAK 13(6Q26) WILD-TYPE   2    0  11   34   19  2   6    2    7   9   1
                             vv
clus                          T4 TX
  DEL PEAK 13(6Q26) MUTATED    0  2
  DEL PEAK 13(6Q26) WILD-TYPE  1  5
D36V40, multiclass
      clus
vv     DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  T1A                          0                           2
  T1A1                         1                           0
  T1B                         11                          11
  T1B1                        17                          34
  T1B2                         2                          19
  T2                           1                           2
  T2A                          0                           6
  T2A1                         4                           2
  T2A2                         1                           7
  T2B                          4                           9
  T3B                          1                           1
  T4                           0                           1
  TX                           2                           5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V41, continuous

Clustering(37) Variable = DEL PEAK 14(7Q34) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(7Q34) MUTATED    27  13
  DEL PEAK 14(7Q34) WILD-TYPE 110  19
  DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE 
                         40                         129 
  DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE 
                         13                          19 
$`DEL PEAK 14(7Q34) MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 
       11.44        68.84         5.46        67.46        31.40        35.01 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ 
       38.99        35.61        40.93        73.45        83.05       100.14 
TCGA-C5-A3HD TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7X5 TCGA-DS-A7WH 
       52.01        25.35        15.48         9.67        13.61         7.33 
TCGA-EA-A1QS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 
        0.76         0.62        14.50        14.96        13.48        45.96 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A2QG 
        0.03         0.36         2.24         0.10        20.35         0.92 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-JW-A5VG TCGA-MU-A51Y TCGA-MY-A5BF 
        1.35         1.97        21.67        14.43        13.87         4.34 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-RA-A741 TCGA-UC-A7PF 
        3.45         3.39         3.88        93.99 

$`DEL PEAK 14(7Q34) 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-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M8 
      177.04       173.29        82.85        19.86        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       57.73        53.16         0.46         2.43         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF 
       73.18        78.35        38.43         0.82        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UC 
       20.42       182.93       101.82       134.33        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       85.55        60.69        94.95         9.34         2.73        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.83        16.18         8.28        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.82        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-EK-A2GZ TCGA-EK-A2IP 
       13.91         0.69        14.99        13.58        12.59         6.64 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.53         0.59         0.07         4.04         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.07         0.10         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       14.70         4.47         6.12         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-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        3.52         1.32         1.12        25.41        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ 
       78.71        81.96        26.56        36.36        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.07         0.82         0.03         5.42        29.72         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        2.96         3.72         5.85         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD 
        6.25        19.59        11.67 

  DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE 
                       0.03                        0.03 
  DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE 
                     100.14                      182.93 
  DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE 
                      14.15                       12.82 
[1] "0.0 - 100.1 (14.1)" "0.0 - 182.9 (12.8)"
[1] "hr=" "2.6"
D37V2, continuous
                             vv
clus                          T1 T2+T3+T4
  DEL PEAK 14(7Q34) MUTATED   16        9
  DEL PEAK 14(7Q34) WILD-TYPE 81       30
D37V3, multiclass
          clus
vv         DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  T1                              16                          81
  T2+T3+T4                         9                          30
[1] 2 2
[1] FALSE
D37V4, binary
                             cls
clus                           0  1
  DEL PEAK 14(7Q34) MUTATED   11 11
  DEL PEAK 14(7Q34) WILD-TYPE 76 29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(7Q34) MUTATED     11   11
  DEL PEAK 14(7Q34) WILD-TYPE   76   29
   clus
vv  DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  0                        11                          76
  1                        11                          29
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK 14(7Q34) MUTATED    9  0 17
  DEL PEAK 14(7Q34) WILD-TYPE 63  3 48
D37V5, multiclass
    clus
vv   DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  M0                         9                          63
  M1                         0                           3
  MX                        17                          48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(7Q34) MUTATED               0                               35
  DEL PEAK 14(7Q34) WILD-TYPE             2                              109
                             vv
clus                          ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 14(7Q34) MUTATED                                               1
  DEL PEAK 14(7Q34) WILD-TYPE                                             3
                             vv
clus                          ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 14(7Q34) MUTATED                                     4
  DEL PEAK 14(7Q34) WILD-TYPE                                  16
                             vv
clus                          ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 14(7Q34) MUTATED                                           0
  DEL PEAK 14(7Q34) WILD-TYPE                                         2
                             vv
clus                          MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 14(7Q34) MUTATED                                              0
  DEL PEAK 14(7Q34) WILD-TYPE                                            4
D37V6, multiclass
                                               clus
vv                                              DEL PEAK 14(7Q34) 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                          0
                                               clus
vv                                              DEL PEAK 14(7Q34) WILD-TYPE
  ADENOSQUAMOUS                                                           2
  CERVICAL SQUAMOUS CELL CARCINOMA                                      109
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           3
  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"
D37V7, binary
                             cls
clus                            0   1
  DEL PEAK 14(7Q34) MUTATED    11  29
  DEL PEAK 14(7Q34) WILD-TYPE  16 120
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(7Q34) MUTATED     11   29
  DEL PEAK 14(7Q34) WILD-TYPE   16  120
     clus
vv    DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  NO                         11                          16
  YES                        29                         120
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(7Q34) MUTATED                                  2     3
  DEL PEAK 14(7Q34) WILD-TYPE                                5    12
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(7Q34) MUTATED                           5
  DEL PEAK 14(7Q34) WILD-TYPE                        13
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(7Q34) MUTATED                                           0    29
  DEL PEAK 14(7Q34) WILD-TYPE                                         1   101
D37V10, multiclass
                                           clus
vv                                          DEL PEAK 14(7Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             3
  BLACK OR AFRICAN AMERICAN                                         5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            29
                                           clus
vv                                          DEL PEAK 14(7Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    5
  ASIAN                                                              12
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             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"
D37V11, binary
                             cls
clus                           0  1
  DEL PEAK 14(7Q34) MUTATED    2 32
  DEL PEAK 14(7Q34) WILD-TYPE  9 95
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(7Q34) MUTATED      2   32
  DEL PEAK 14(7Q34) WILD-TYPE    9   95
                        clus
vv                       DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             2                           9
  NOT HISPANIC OR LATINO                        32                          95
[1] 2 2
[1] FALSE
D37V12, continuous
D37V13, binary
                             cls
clus                           0  1
  DEL PEAK 14(7Q34) MUTATED    7 11
  DEL PEAK 14(7Q34) WILD-TYPE 41  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(7Q34) MUTATED      7   11
  DEL PEAK 14(7Q34) WILD-TYPE   41    8
            clus
vv           DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  TUMOR FREE                         7                          41
  WITH TUMOR                        11                           8
[1] 2 2
[1] FALSE
                             vv
clus                          NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 14(7Q34) MUTATED         0      2       0            35       3
  DEL PEAK 14(7Q34) WILD-TYPE       1      8       6           112       9
D37V14, multiclass
               clus
vv              DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  NIGERIA                               0                           1
  RUSSIA                                2                           8
  UKRAINE                               0                           6
  UNITED STATES                        35                         112
  VIETNAM                               3                           9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          G1 G2 G3 G4 GX
  DEL PEAK 14(7Q34) MUTATED    2 19 17  0  2
  DEL PEAK 14(7Q34) WILD-TYPE 12 64 55  1  3
D37V15, multiclass
    clus
vv   DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  G1                         2                          12
  G2                        19                          64
  G3                        17                          55
  G4                         0                           1
  GX                         2                           3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V16, continuous
D37V17, continuous
                             vv
clus                          CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 14(7Q34) MUTATED                                             4
  DEL PEAK 14(7Q34) WILD-TYPE                                          17
                             vv
clus                          CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 14(7Q34) MUTATED                                        2
  DEL PEAK 14(7Q34) WILD-TYPE                                      6
                             vv
clus                          CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 14(7Q34) MUTATED                                                 0
  DEL PEAK 14(7Q34) WILD-TYPE                                               1
                             vv
clus                          CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 14(7Q34) MUTATED               10                  17
  DEL PEAK 14(7Q34) WILD-TYPE             26                  66
D37V18, multiclass
                                                 clus
vv                                                DEL PEAK 14(7Q34) 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                                                         10
  LIFELONG NON-SMOKER                                                    17
                                                 clus
vv                                                DEL PEAK 14(7Q34) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           1
  CURRENT SMOKER                                                           26
  LIFELONG NON-SMOKER                                                      66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V19, continuous
                             vv
clus                          COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 14(7Q34) MUTATED             8        6             3        2
  DEL PEAK 14(7Q34) WILD-TYPE           9       31             8        3
D37V20, multiclass
               clus
vv              DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  COMBINATION                           8                           9
  EXTERNAL                              6                          31
  EXTERNAL BEAM                         3                           8
  INTERNAL                              2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V21, binary
                             cls
clus                          0 1
  DEL PEAK 14(7Q34) MUTATED   4 2
  DEL PEAK 14(7Q34) WILD-TYPE 7 1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(7Q34) MUTATED      4    2
  DEL PEAK 14(7Q34) WILD-TYPE    7    1
     clus
vv    DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  CGY                         4                           7
  GY                          2                           1
[1] 2 2
[1] FALSE
D37V22, continuous
D37V23, continuous
D37V24, continuous
D37V25, continuous
D37V26, continuous
D37V27, continuous
                             vv
clus                          MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 14(7Q34) MUTATED                                     0
  DEL PEAK 14(7Q34) WILD-TYPE                                   2
                             vv
clus                          MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 14(7Q34) MUTATED                                     2
  DEL PEAK 14(7Q34) WILD-TYPE                                   4
                             vv
clus                          OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 14(7Q34) MUTATED                         1                       0
  DEL PEAK 14(7Q34) WILD-TYPE                       8                       1
                             vv
clus                          POSITIVE VAGINAL MARGIN
  DEL PEAK 14(7Q34) MUTATED                         1
  DEL PEAK 14(7Q34) WILD-TYPE                       4
D37V28, multiclass
                                     clus
vv                                    DEL PEAK 14(7Q34) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                         0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                         2
  OTHER LOCATION, SPECIFY                                     1
  POSITIVE BLADDER MARGIN                                     0
  POSITIVE VAGINAL MARGIN                                     1
                                     clus
vv                                    DEL PEAK 14(7Q34) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                       8
  POSITIVE BLADDER MARGIN                                       1
  POSITIVE VAGINAL MARGIN                                       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)
  DEL PEAK 14(7Q34) MUTATED                                               1
  DEL PEAK 14(7Q34) WILD-TYPE                                             1
                             vv
clus                          PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 14(7Q34) MUTATED                                                4
  DEL PEAK 14(7Q34) WILD-TYPE                                              6
                             vv
clus                          POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 14(7Q34) MUTATED                                                                                  12
  DEL PEAK 14(7Q34) WILD-TYPE                                                                                42
                             vv
clus                          PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 14(7Q34) MUTATED                                                                                             16
  DEL PEAK 14(7Q34) WILD-TYPE                                                                                           61
D37V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 14(7Q34) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                        1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                       4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                   12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                        16
                                                                                              clus
vv                                                                                             DEL PEAK 14(7Q34) 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)                                     42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V30, binary
                             cls
clus                           0  1
  DEL PEAK 14(7Q34) MUTATED    6 18
  DEL PEAK 14(7Q34) WILD-TYPE 48 41
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(7Q34) MUTATED      6   18
  DEL PEAK 14(7Q34) WILD-TYPE   48   41
         clus
vv        DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  ABSENT                          6                          48
  PRESENT                        18                          41
[1] 2 2
[1] FALSE
D37V31, continuous
D37V32, continuous
D37V33, binary
                             cls
clus                           0  1
  DEL PEAK 14(7Q34) MUTATED   12 17
  DEL PEAK 14(7Q34) WILD-TYPE 23 64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(7Q34) MUTATED     12   17
  DEL PEAK 14(7Q34) WILD-TYPE   23   64
                                          clus
vv                                         DEL PEAK 14(7Q34) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                            12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                        17
                                          clus
vv                                         DEL PEAK 14(7Q34) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                              23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          64
[1] 2 2
[1] FALSE
D37V34, continuous
                             vv
clus                          OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 14(7Q34) MUTATED       1                   23                   0
  DEL PEAK 14(7Q34) WILD-TYPE     2                   90                   5
D37V35, multiclass
                      clus
vv                     DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  OTHER                                        1                           2
  RADICAL HYSTERECTOMY                        23                          90
  SIMPLE HYSTERECTOMY                          0                           5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CURRENT USER FORMER USER NEVER USED
  DEL PEAK 14(7Q34) MUTATED              1          10          6
  DEL PEAK 14(7Q34) WILD-TYPE            7          30         34
D37V36, multiclass
              clus
vv             DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  CURRENT USER                         1                           7
  FORMER USER                         10                          30
  NEVER USED                           6                          34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V37, continuous
D37V38, binary
                             cls
clus                           0  1
  DEL PEAK 14(7Q34) MUTATED   14  3
  DEL PEAK 14(7Q34) WILD-TYPE 59 11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(7Q34) MUTATED     14    3
  DEL PEAK 14(7Q34) WILD-TYPE   59   11
         clus
vv        DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  ABSENT                         14                          59
  PRESENT                         3                          11
[1] 2 2
[1] FALSE
D37V39, continuous
                             vv
clus                          T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 14(7Q34) MUTATED     0    0   5   10    1  1   1    3    2   1   1
  DEL PEAK 14(7Q34) WILD-TYPE   2    1  17   41   20  2   5    3    6  12   1
                             vv
clus                          T4 TX
  DEL PEAK 14(7Q34) MUTATED    0  2
  DEL PEAK 14(7Q34) WILD-TYPE  1  5
D37V40, multiclass
      clus
vv     DEL PEAK 14(7Q34) MUTATED DEL PEAK 14(7Q34) WILD-TYPE
  T1A                          0                           2
  T1A1                         0                           1
  T1B                          5                          17
  T1B1                        10                          41
  T1B2                         1                          20
  T2                           1                           2
  T2A                          1                           5
  T2A1                         3                           3
  T2A2                         2                           6
  T2B                          1                          12
  T3B                          1                           1
  T4                           0                           1
  TX                           2                           5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V41, continuous

Clustering(38) Variable = DEL PEAK 15(8P23.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(8P23.3) MUTATED   44 15
  DEL PEAK 15(8P23.3) WILD-TYPE 93 17
  DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE 
                           59                           110 
  DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE 
                           15                            17 
$`DEL PEAK 15(8P23.3) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
       57.04        68.84         5.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LT 
       35.01        57.73        53.16         2.43        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CK TCGA-C5-A7UH 
       73.45        78.35         0.82        52.01       134.33        60.69 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WI 
       94.95        13.61         2.73        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-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
       12.59        45.96         2.24         0.07         0.10         0.03 
TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB 
        6.94         6.12         1.22        23.84         1.45         0.82 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LA 
        1.32         1.12        25.41        21.67        14.93       137.16 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A5U3 
       78.71        26.56        15.58         5.13         0.89         0.82 
TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PD 
        0.03         2.96         3.39        19.59        11.67 

$`DEL PEAK 15(8P23.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        23.67        11.44        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1MH 
      177.04       173.29        82.85        19.86        67.46        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ 
       35.61         0.46         3.58        44.22        83.05       100.14 
TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       38.43        18.02        17.85        20.42       182.93        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7X3 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
        9.34        87.75        58.88         2.66       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS 
       16.83        16.18         7.33         0.76         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26         1.48        13.91         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       14.96        13.58        13.48         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.10        20.35         7.92        14.70         4.47 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17         0.66         1.02         1.58         1.48 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 
        3.52         1.35         1.97        20.78         4.11       147.39 
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        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AX 
       16.64        19.33        20.48        10.06         0.10         0.07 
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         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        3.45         5.85         3.72         5.75         4.80         6.25 
TCGA-RA-A741 TCGA-UC-A7PF 
        3.88        93.99 

  DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE 
                         0.03                          0.03 
  DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE 
                       137.16                        182.93 
  DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE 
                       14.500                        13.265 
[1] "0.0 - 137.2 (14.5)" "0.0 - 182.9 (13.3)"
[1] "hr=" "1.5"
D38V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK 15(8P23.3) MUTATED   32       13
  DEL PEAK 15(8P23.3) WILD-TYPE 65       26
D38V3, multiclass
          clus
vv         DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  T1                                32                            65
  T2+T3+T4                          13                            26
[1] 2 2
[1] FALSE
D38V4, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.3) MUTATED   30 13
  DEL PEAK 15(8P23.3) WILD-TYPE 57 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.3) MUTATED     30   13
  DEL PEAK 15(8P23.3) WILD-TYPE   57   27
   clus
vv  DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  0                          30                            57
  1                          13                            27
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 15(8P23.3) MUTATED   25  0 20
  DEL PEAK 15(8P23.3) WILD-TYPE 47  3 45
D38V5, multiclass
    clus
vv   DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  M0                          25                            47
  M1                           0                             3
  MX                          20                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(8P23.3) MUTATED               0                               53
  DEL PEAK 15(8P23.3) WILD-TYPE             2                               91
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 15(8P23.3) MUTATED                                               1
  DEL PEAK 15(8P23.3) WILD-TYPE                                             3
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 15(8P23.3) MUTATED                                     5
  DEL PEAK 15(8P23.3) WILD-TYPE                                  15
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 15(8P23.3) MUTATED                                           2
  DEL PEAK 15(8P23.3) WILD-TYPE                                         0
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 15(8P23.3) MUTATED                                              1
  DEL PEAK 15(8P23.3) WILD-TYPE                                            3
D38V6, multiclass
                                               clus
vv                                              DEL PEAK 15(8P23.3) MUTATED
  ADENOSQUAMOUS                                                           0
  CERVICAL SQUAMOUS CELL CARCINOMA                                       53
  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                                              DEL PEAK 15(8P23.3) WILD-TYPE
  ADENOSQUAMOUS                                                             2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         91
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.3) MUTATED   12 50
  DEL PEAK 15(8P23.3) WILD-TYPE 15 99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.3) MUTATED     12   50
  DEL PEAK 15(8P23.3) WILD-TYPE   15   99
     clus
vv    DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  NO                           12                            15
  YES                          50                            99
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(8P23.3) MUTATED                                  3     3
  DEL PEAK 15(8P23.3) WILD-TYPE                                4    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(8P23.3) MUTATED                           8
  DEL PEAK 15(8P23.3) WILD-TYPE                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(8P23.3) MUTATED                                           1    47
  DEL PEAK 15(8P23.3) WILD-TYPE                                         0    83
D38V10, multiclass
                                           clus
vv                                          DEL PEAK 15(8P23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              47
                                           clus
vv                                          DEL PEAK 15(8P23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                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"
D38V11, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.3) MUTATED    4 45
  DEL PEAK 15(8P23.3) WILD-TYPE  7 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.3) MUTATED      4   45
  DEL PEAK 15(8P23.3) WILD-TYPE    7   82
                        clus
vv                       DEL PEAK 15(8P23.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       DEL PEAK 15(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            82
[1] 2 2
[1] FALSE
D38V12, continuous
D38V13, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.3) MUTATED   20  8
  DEL PEAK 15(8P23.3) WILD-TYPE 28 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.3) MUTATED     20    8
  DEL PEAK 15(8P23.3) WILD-TYPE   28   11
            clus
vv           DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  TUMOR FREE                          20                            28
  WITH TUMOR                           8                            11
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 15(8P23.3) MUTATED         1      3       2            53       3
  DEL PEAK 15(8P23.3) WILD-TYPE       0      7       4            94       9
D38V14, multiclass
               clus
vv              DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  NIGERIA                                 1                             0
  RUSSIA                                  3                             7
  UKRAINE                                 2                             4
  UNITED STATES                          53                            94
  VIETNAM                                 3                             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 15(8P23.3) MUTATED    4 27 29  1  1
  DEL PEAK 15(8P23.3) WILD-TYPE 10 56 43  0  4
D38V15, multiclass
    clus
vv   DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  G1                           4                            10
  G2                          27                            56
  G3                          29                            43
  G4                           1                             0
  GX                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V16, continuous
D38V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 15(8P23.3) MUTATED                                             8
  DEL PEAK 15(8P23.3) WILD-TYPE                                          13
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 15(8P23.3) MUTATED                                        3
  DEL PEAK 15(8P23.3) WILD-TYPE                                      5
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 15(8P23.3) MUTATED                                                 1
  DEL PEAK 15(8P23.3) WILD-TYPE                                               0
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 15(8P23.3) MUTATED               13                  26
  DEL PEAK 15(8P23.3) WILD-TYPE             23                  57
D38V18, multiclass
                                                 clus
vv                                                DEL PEAK 15(8P23.3) 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                                                           13
  LIFELONG NON-SMOKER                                                      26
                                                 clus
vv                                                DEL PEAK 15(8P23.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             23
  LIFELONG NON-SMOKER                                                        57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 15(8P23.3) MUTATED             7       13             6        2
  DEL PEAK 15(8P23.3) WILD-TYPE          10       24             5        3
D38V20, multiclass
               clus
vv              DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  COMBINATION                             7                            10
  EXTERNAL                               13                            24
  EXTERNAL BEAM                           6                             5
  INTERNAL                                2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V21, binary
                               cls
clus                            0 1
  DEL PEAK 15(8P23.3) MUTATED   5 1
  DEL PEAK 15(8P23.3) WILD-TYPE 6 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.3) MUTATED      5    1
  DEL PEAK 15(8P23.3) WILD-TYPE    6    2
     clus
vv    DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  CGY                           5                             6
  GY                            1                             2
[1] 2 2
[1] FALSE
D38V22, continuous
D38V23, continuous
D38V24, continuous
D38V25, continuous
D38V26, continuous
D38V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 15(8P23.3) MUTATED                                     1
  DEL PEAK 15(8P23.3) WILD-TYPE                                   1
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 15(8P23.3) MUTATED                                     1
  DEL PEAK 15(8P23.3) WILD-TYPE                                   5
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 15(8P23.3) MUTATED                         4                       0
  DEL PEAK 15(8P23.3) WILD-TYPE                       5                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 15(8P23.3) MUTATED                         2
  DEL PEAK 15(8P23.3) WILD-TYPE                       3
D38V28, multiclass
                                     clus
vv                                    DEL PEAK 15(8P23.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           1
  OTHER LOCATION, SPECIFY                                       4
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       2
                                     clus
vv                                    DEL PEAK 15(8P23.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             5
  OTHER LOCATION, SPECIFY                                         5
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK 15(8P23.3) MUTATED                                               1
  DEL PEAK 15(8P23.3) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 15(8P23.3) MUTATED                                                2
  DEL PEAK 15(8P23.3) WILD-TYPE                                              8
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 15(8P23.3) MUTATED                                                                                  16
  DEL PEAK 15(8P23.3) WILD-TYPE                                                                                38
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 15(8P23.3) MUTATED                                                                                             32
  DEL PEAK 15(8P23.3) WILD-TYPE                                                                                           45
D38V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 15(8P23.3) 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)                                     16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                          32
                                                                                              clus
vv                                                                                             DEL PEAK 15(8P23.3) 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)                                       38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V30, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.3) MUTATED   22 18
  DEL PEAK 15(8P23.3) WILD-TYPE 32 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.3) MUTATED     22   18
  DEL PEAK 15(8P23.3) WILD-TYPE   32   41
         clus
vv        DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  ABSENT                           22                            32
  PRESENT                          18                            41
[1] 2 2
[1] FALSE
D38V31, continuous
D38V32, continuous
D38V33, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.3) MUTATED   14 27
  DEL PEAK 15(8P23.3) WILD-TYPE 21 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.3) MUTATED     14   27
  DEL PEAK 15(8P23.3) WILD-TYPE   21   54
                                          clus
vv                                         DEL PEAK 15(8P23.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          27
                                          clus
vv                                         DEL PEAK 15(8P23.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            54
[1] 2 2
[1] FALSE
D38V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 15(8P23.3) MUTATED       0                   39                   1
  DEL PEAK 15(8P23.3) WILD-TYPE     3                   74                   4
D38V35, multiclass
                      clus
vv                     DEL PEAK 15(8P23.3) MUTATED
  OTHER                                          0
  RADICAL HYSTERECTOMY                          39
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     DEL PEAK 15(8P23.3) WILD-TYPE
  OTHER                                            3
  RADICAL HYSTERECTOMY                            74
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 15(8P23.3) MUTATED              2          18         15
  DEL PEAK 15(8P23.3) WILD-TYPE            6          22         25
D38V36, multiclass
              clus
vv             DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  CURRENT USER                           2                             6
  FORMER USER                           18                            22
  NEVER USED                            15                            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"
D38V37, continuous
D38V38, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.3) MUTATED   27  4
  DEL PEAK 15(8P23.3) WILD-TYPE 46 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.3) MUTATED     27    4
  DEL PEAK 15(8P23.3) WILD-TYPE   46   10
         clus
vv        DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  ABSENT                           27                            46
  PRESENT                           4                            10
[1] 2 2
[1] FALSE
D38V39, continuous
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 15(8P23.3) MUTATED     2    1   8   13    8  0   2    4    4   2   1
  DEL PEAK 15(8P23.3) WILD-TYPE   0    0  14   38   13  3   4    2    4  11   1
                               vv
clus                            T4 TX
  DEL PEAK 15(8P23.3) MUTATED    0  2
  DEL PEAK 15(8P23.3) WILD-TYPE  1  5
D38V40, multiclass
      clus
vv     DEL PEAK 15(8P23.3) MUTATED DEL PEAK 15(8P23.3) WILD-TYPE
  T1A                            2                             0
  T1A1                           1                             0
  T1B                            8                            14
  T1B1                          13                            38
  T1B2                           8                            13
  T2                             0                             3
  T2A                            2                             4
  T2A1                           4                             2
  T2A2                           4                             4
  T2B                            2                            11
  T3B                            1                             1
  T4                             0                             1
  TX                             2                             5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V41, continuous

Clustering(39) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D39V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 16(10Q23.31) MUTATED    35  14
  DEL PEAK 16(10Q23.31) WILD-TYPE 102  18
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             49                             120 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             14                              18 
$`DEL PEAK 16(10Q23.31) 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-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       38.99        35.61         0.46        73.18        73.45        83.05 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93        25.35       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-EA-A439 
       73.41        17.19        13.61         2.73        36.76        14.50 
TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-EK-A2RL 
       14.96        13.48        12.59         6.64         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.24         0.10        20.35         0.92         1.58         1.48 
TCGA-FU-A40J TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3LB TCGA-IR-A3LH 
        1.35        21.67        20.78         4.11        66.81        78.71 
TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-A69B TCGA-LP-A4AX TCGA-PN-A8MA TCGA-Q1-A5R2 
       36.36        20.48        10.06         0.07         2.96         3.45 
TCGA-Q1-A6DT 
        3.39 

$`DEL PEAK 16(10Q23.31) 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-A7CJ TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       17.85       101.82        85.55        60.69        94.95         9.34 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       87.75        58.88         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50         1.35         1.35         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.26        14.89         1.48        13.91         0.69        14.99 
TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       13.58        45.96         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.03         0.36         0.07         0.10         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70         4.47         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB 
       23.84         2.17         0.66         1.02         1.45         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A4S6 
        3.52         1.32         1.97         1.12        25.41        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
      147.39       137.16       117.40        96.95        81.96        26.56 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU 
       14.43        16.64        19.33        15.58         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.89         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        0.07         4.34         3.72         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         182.93                          177.04 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         17.190                          12.015 
[1] "0.1 - 182.9 (17.2)" "0.0 - 177.0 (12.0)"
[1] "hr=" "1.8"
D39V2, continuous
                                 vv
clus                              T1 T2+T3+T4
  DEL PEAK 16(10Q23.31) MUTATED   25       12
  DEL PEAK 16(10Q23.31) WILD-TYPE 72       27
D39V3, multiclass
          clus
vv         DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T1                                  25                              72
  T2+T3+T4                            12                              27
[1] 2 2
[1] FALSE
D39V4, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   19 14
  DEL PEAK 16(10Q23.31) WILD-TYPE 68 26
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     19   14
  DEL PEAK 16(10Q23.31) WILD-TYPE   68   26
   clus
vv  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  0                            19                              68
  1                            14                              26
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 16(10Q23.31) MUTATED   16  1 21
  DEL PEAK 16(10Q23.31) WILD-TYPE 56  2 44
D39V5, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  M0                            16                              56
  M1                             1                               2
  MX                            21                              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 16(10Q23.31) MUTATED               1
  DEL PEAK 16(10Q23.31) WILD-TYPE             1
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(10Q23.31) MUTATED                                 44
  DEL PEAK 16(10Q23.31) WILD-TYPE                              100
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 16(10Q23.31) MUTATED                                               1
  DEL PEAK 16(10Q23.31) WILD-TYPE                                             3
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 16(10Q23.31) MUTATED                                     6
  DEL PEAK 16(10Q23.31) WILD-TYPE                                  14
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 16(10Q23.31) MUTATED                                           0
  DEL PEAK 16(10Q23.31) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 16(10Q23.31) MUTATED                                              1
  DEL PEAK 16(10Q23.31) WILD-TYPE                                            3
D39V6, multiclass
                                               clus
vv                                              DEL PEAK 16(10Q23.31) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              1
                                               clus
vv                                              DEL PEAK 16(10Q23.31) WILD-TYPE
  ADENOSQUAMOUS                                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                                          100
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        14
  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"
D39V7, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    11  42
  DEL PEAK 16(10Q23.31) WILD-TYPE  16 107
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     11   42
  DEL PEAK 16(10Q23.31) WILD-TYPE   16  107
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  NO                             11                              16
  YES                            42                             107
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(10Q23.31) MUTATED                                  0     4
  DEL PEAK 16(10Q23.31) WILD-TYPE                                7    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(10Q23.31) MUTATED                          12
  DEL PEAK 16(10Q23.31) WILD-TYPE                         6
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 16(10Q23.31) MUTATED                                           0
  DEL PEAK 16(10Q23.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 16(10Q23.31) MUTATED      36
  DEL PEAK 16(10Q23.31) WILD-TYPE    94
D39V10, multiclass
                                           clus
vv                                          DEL PEAK 16(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 4
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                36
                                           clus
vv                                          DEL PEAK 16(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  11
  BLACK OR AFRICAN AMERICAN                                               6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                  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"
D39V11, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    3 37
  DEL PEAK 16(10Q23.31) WILD-TYPE  8 90
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      3   37
  DEL PEAK 16(10Q23.31) WILD-TYPE    8   90
                        clus
vv                       DEL PEAK 16(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            37
                        clus
vv                       DEL PEAK 16(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                              90
[1] 2 2
[1] FALSE
D39V12, continuous
D39V13, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   15  6
  DEL PEAK 16(10Q23.31) WILD-TYPE 33 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     15    6
  DEL PEAK 16(10Q23.31) WILD-TYPE   33   13
            clus
vv           DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  TUMOR FREE                            15                              33
  WITH TUMOR                             6                              13
[1] 2 2
[1] FALSE
                                 vv
clus                              NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 16(10Q23.31) MUTATED         1      0       0            48       4
  DEL PEAK 16(10Q23.31) WILD-TYPE       0     10       6            99       8
D39V14, multiclass
               clus
vv              DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  NIGERIA                                   1                               0
  RUSSIA                                    0                              10
  UKRAINE                                   0                               6
  UNITED STATES                            48                              99
  VIETNAM                                   4                               8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 16(10Q23.31) MUTATED    0 23 27  1  2
  DEL PEAK 16(10Q23.31) WILD-TYPE 14 60 45  0  3
D39V15, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  G1                             0                              14
  G2                            23                              60
  G3                            27                              45
  G4                             1                               0
  GX                             2                               3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V16, continuous
D39V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 16(10Q23.31) MUTATED                                             8
  DEL PEAK 16(10Q23.31) WILD-TYPE                                          13
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 16(10Q23.31) MUTATED                                        4
  DEL PEAK 16(10Q23.31) WILD-TYPE                                      4
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 16(10Q23.31) MUTATED                                                 1
  DEL PEAK 16(10Q23.31) WILD-TYPE                                               0
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 16(10Q23.31) MUTATED               10                  16
  DEL PEAK 16(10Q23.31) WILD-TYPE             26                  67
D39V18, multiclass
                                                 clus
vv                                                DEL PEAK 16(10Q23.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             10
  LIFELONG NON-SMOKER                                                        16
                                                 clus
vv                                                DEL PEAK 16(10Q23.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               0
  CURRENT SMOKER                                                               26
  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"
D39V19, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 16(10Q23.31) MUTATED             5       11             6        2
  DEL PEAK 16(10Q23.31) WILD-TYPE          12       26             5        3
D39V20, multiclass
               clus
vv              DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  COMBINATION                               5                              12
  EXTERNAL                                 11                              26
  EXTERNAL BEAM                             6                               5
  INTERNAL                                  2                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V21, binary
                                 cls
clus                              0 1
  DEL PEAK 16(10Q23.31) MUTATED   5 1
  DEL PEAK 16(10Q23.31) WILD-TYPE 6 2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      5    1
  DEL PEAK 16(10Q23.31) WILD-TYPE    6    2
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CGY                             5                               6
  GY                              1                               2
[1] 2 2
[1] FALSE
D39V22, continuous
D39V23, continuous
D39V24, continuous
D39V25, continuous
D39V26, continuous
D39V27, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 16(10Q23.31) MUTATED                                     0
  DEL PEAK 16(10Q23.31) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 16(10Q23.31) MUTATED                                     3
  DEL PEAK 16(10Q23.31) WILD-TYPE                                   3
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 16(10Q23.31) MUTATED                         1
  DEL PEAK 16(10Q23.31) WILD-TYPE                       8
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 16(10Q23.31) MUTATED                         0
  DEL PEAK 16(10Q23.31) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 16(10Q23.31) MUTATED                         4
  DEL PEAK 16(10Q23.31) WILD-TYPE                       1
D39V28, multiclass
                                     clus
vv                                    DEL PEAK 16(10Q23.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             3
  OTHER LOCATION, SPECIFY                                         1
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         4
                                     clus
vv                                    DEL PEAK 16(10Q23.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               3
  OTHER LOCATION, SPECIFY                                           8
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 16(10Q23.31) MUTATED                                               0
  DEL PEAK 16(10Q23.31) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 16(10Q23.31) MUTATED                                                5
  DEL PEAK 16(10Q23.31) WILD-TYPE                                              5
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 16(10Q23.31) MUTATED                                                                                  21
  DEL PEAK 16(10Q23.31) WILD-TYPE                                                                                33
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 16(10Q23.31) MUTATED                                                                                             13
  DEL PEAK 16(10Q23.31) WILD-TYPE                                                                                           64
D39V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 16(10Q23.31) 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)                                       21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            13
                                                                                              clus
vv                                                                                             DEL PEAK 16(10Q23.31) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                             5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V30, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   12 20
  DEL PEAK 16(10Q23.31) WILD-TYPE 42 39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     12   20
  DEL PEAK 16(10Q23.31) WILD-TYPE   42   39
         clus
vv        DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  ABSENT                             12                              42
  PRESENT                            20                              39
[1] 2 2
[1] FALSE
D39V31, continuous
D39V32, continuous
D39V33, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   16 19
  DEL PEAK 16(10Q23.31) WILD-TYPE 19 62
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     16   19
  DEL PEAK 16(10Q23.31) WILD-TYPE   19   62
                                          clus
vv                                         DEL PEAK 16(10Q23.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                16
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            19
                                          clus
vv                                         DEL PEAK 16(10Q23.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              62
[1] 2 2
[1] FALSE
D39V34, continuous
                                 vv
clus                              OTHER RADICAL HYSTERECTOMY
  DEL PEAK 16(10Q23.31) MUTATED       1                   33
  DEL PEAK 16(10Q23.31) WILD-TYPE     2                   80
                                 vv
clus                              SIMPLE HYSTERECTOMY
  DEL PEAK 16(10Q23.31) MUTATED                     1
  DEL PEAK 16(10Q23.31) WILD-TYPE                   4
D39V35, multiclass
                      clus
vv                     DEL PEAK 16(10Q23.31) MUTATED
  OTHER                                            1
  RADICAL HYSTERECTOMY                            33
  SIMPLE HYSTERECTOMY                              1
                      clus
vv                     DEL PEAK 16(10Q23.31) WILD-TYPE
  OTHER                                              2
  RADICAL HYSTERECTOMY                              80
  SIMPLE HYSTERECTOMY                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 16(10Q23.31) MUTATED              1           9          9
  DEL PEAK 16(10Q23.31) WILD-TYPE            7          31         31
D39V36, multiclass
              clus
vv             DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CURRENT USER                             1                               7
  FORMER USER                              9                              31
  NEVER USED                               9                              31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V37, continuous
D39V38, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   16  5
  DEL PEAK 16(10Q23.31) WILD-TYPE 57  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     16    5
  DEL PEAK 16(10Q23.31) WILD-TYPE   57    9
         clus
vv        DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  ABSENT                             16                              57
  PRESENT                             5                               9
[1] 2 2
[1] FALSE
D39V39, continuous
[1] "Remove cluster labels:"        "DEL PEAK 16(10Q23.31) MUTATED"
clus
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              2                               7 
                     TCGA-C5-A1BN                      TCGA-C5-A1MN 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-C5-A1MP                      TCGA-EK-A2RO 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-JW-A852                      TCGA-MU-A51Y 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-MU-A8JM 
"DEL PEAK 16(10Q23.31) WILD-TYPE" 
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 16(10Q23.31) MUTATED     0    0   5   15    5  2   2    3    0   5
  DEL PEAK 16(10Q23.31) WILD-TYPE   2    1  17   36   16  1   4    3    8   8
                                 vv
clus                              T3B T4 TX
  DEL PEAK 16(10Q23.31) MUTATED     0  0  2
  DEL PEAK 16(10Q23.31) WILD-TYPE   2  1  5
D39V40, multiclass
      clus
vv     DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T1A                              0                               2
  T1A1                             0                               1
  T1B                              5                              17
  T1B1                            15                              36
  T1B2                             5                              16
  T2                               2                               1
  T2A                              2                               4
  T2A1                             3                               3
  T2A2                             0                               8
  T2B                              5                               8
  T3B                              0                               2
  T4                               0                               1
  TX                               2                               5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V41, continuous

Clustering(40) Variable = DEL PEAK 17(11P15.1) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(11P15.1) MUTATED   40 14
  DEL PEAK 17(11P15.1) WILD-TYPE 97 18
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            54                            115 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                            14                             18 
$`DEL PEAK 17(11P15.1) MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M7 
       49.48        18.74       177.04         5.46        19.86        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LV TCGA-C5-A2LZ 
       30.21        38.99        35.61         0.46        73.45       100.14 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 
      182.93        25.35        15.48        60.69        94.95         2.73 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A411 
       87.75        36.76       117.99       118.65        12.36         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.50         1.81        12.66         0.26        14.99        14.96 
TCGA-EA-A78R TCGA-EK-A2PG TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A69M 
       13.48         0.53         2.24         0.10        20.35         6.12 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-FU-A770 TCGA-IR-A3LB TCGA-IR-A3LC 
       23.84         1.45         0.82         1.12        66.81       117.40 
TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AX 
       26.56        16.64        19.33        20.48         0.10         0.07 
TCGA-LP-A5U3 TCGA-MY-A5BE TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-R2-A69V 
        0.82         0.07         3.45         3.39         5.75        19.59 

$`DEL PEAK 17(11P15.1) 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-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME 
      173.29        82.85        67.46        31.40        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         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZM TCGA-DS-A0VL 
       17.19        85.55         9.34        13.61        58.88         2.66 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50         1.35        12.82        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 
        0.69        13.58        12.59        45.96         6.64         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.07         0.10         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       14.70         4.47         1.22         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.02         1.58         1.48         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.97        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL 
      147.39       137.16        96.95        78.71        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AW TCGA-MU-A51Y 
       14.43        15.58        10.06         5.13         0.89        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        0.03         5.42        29.72         4.34         2.96         3.72 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD 
        5.85         3.72         4.80         6.25         3.88        11.67 
TCGA-UC-A7PF 
       93.99 

  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                        182.93                         173.29 
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                         16.06                          11.67 
[1] "0.1 - 182.9 (16.1)" "0.0 - 173.3 (11.7)"
[1] "hr=" "1.3"
D40V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 17(11P15.1) MUTATED   31       12
  DEL PEAK 17(11P15.1) WILD-TYPE 66       27
D40V3, multiclass
          clus
vv         DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  T1                                 31                             66
  T2+T3+T4                           12                             27
[1] 2 2
[1] FALSE
D40V4, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   27 12
  DEL PEAK 17(11P15.1) WILD-TYPE 60 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     27   12
  DEL PEAK 17(11P15.1) WILD-TYPE   60   28
   clus
vv  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  0                           27                             60
  1                           12                             28
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 17(11P15.1) MUTATED   25  0 21
  DEL PEAK 17(11P15.1) WILD-TYPE 47  3 44
D40V5, multiclass
    clus
vv   DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  M0                           25                             47
  M1                            0                              3
  MX                           21                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(11P15.1) MUTATED               0                               53
  DEL PEAK 17(11P15.1) WILD-TYPE             2                               91
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 17(11P15.1) MUTATED                                               1
  DEL PEAK 17(11P15.1) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 17(11P15.1) MUTATED                                     3
  DEL PEAK 17(11P15.1) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 17(11P15.1) MUTATED                                           0
  DEL PEAK 17(11P15.1) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 17(11P15.1) MUTATED                                              1
  DEL PEAK 17(11P15.1) WILD-TYPE                                            3
D40V6, multiclass
                                               clus
vv                                              DEL PEAK 17(11P15.1) MUTATED
  ADENOSQUAMOUS                                                            0
  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                             1
                                               clus
vv                                              DEL PEAK 17(11P15.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          91
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED    7 51
  DEL PEAK 17(11P15.1) WILD-TYPE 20 98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED      7   51
  DEL PEAK 17(11P15.1) WILD-TYPE   20   98
     clus
vv    DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  NO                             7                             20
  YES                           51                             98
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(11P15.1) MUTATED                                  2    10
  DEL PEAK 17(11P15.1) WILD-TYPE                                5     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(11P15.1) MUTATED                           7
  DEL PEAK 17(11P15.1) WILD-TYPE                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 17(11P15.1) MUTATED                                           1
  DEL PEAK 17(11P15.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 17(11P15.1) MUTATED      38
  DEL PEAK 17(11P15.1) WILD-TYPE    92
D40V10, multiclass
                                           clus
vv                                          DEL PEAK 17(11P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               38
                                           clus
vv                                          DEL PEAK 17(11P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                  5
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"
D40V11, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED    3 45
  DEL PEAK 17(11P15.1) WILD-TYPE  8 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED      3   45
  DEL PEAK 17(11P15.1) WILD-TYPE    8   82
                        clus
vv                       DEL PEAK 17(11P15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           45
                        clus
vv                       DEL PEAK 17(11P15.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             82
[1] 2 2
[1] FALSE
D40V12, continuous
D40V13, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   17  9
  DEL PEAK 17(11P15.1) WILD-TYPE 31 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     17    9
  DEL PEAK 17(11P15.1) WILD-TYPE   31   10
            clus
vv           DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  TUMOR FREE                           17                             31
  WITH TUMOR                            9                             10
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 17(11P15.1) MUTATED         0      2       2            45       9
  DEL PEAK 17(11P15.1) WILD-TYPE       1      8       4           102       3
D40V14, multiclass
               clus
vv              DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  2                              4
  UNITED STATES                           45                            102
  VIETNAM                                  9                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 17(11P15.1) MUTATED    1 24 30  0  2
  DEL PEAK 17(11P15.1) WILD-TYPE 13 59 42  1  3
D40V15, multiclass
    clus
vv   DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  G1                            1                             13
  G2                           24                             59
  G3                           30                             42
  G4                            0                              1
  GX                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V16, continuous
D40V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 17(11P15.1) MUTATED                                             6
  DEL PEAK 17(11P15.1) WILD-TYPE                                          15
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 17(11P15.1) MUTATED                                        3
  DEL PEAK 17(11P15.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 17(11P15.1) MUTATED                                                 0
  DEL PEAK 17(11P15.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 17(11P15.1) MUTATED               13                  31
  DEL PEAK 17(11P15.1) WILD-TYPE             23                  52
D40V18, multiclass
                                                 clus
vv                                                DEL PEAK 17(11P15.1) 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                                                            13
  LIFELONG NON-SMOKER                                                       31
                                                 clus
vv                                                DEL PEAK 17(11P15.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              23
  LIFELONG NON-SMOKER                                                         52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 17(11P15.1) MUTATED             4       11             3        2
  DEL PEAK 17(11P15.1) WILD-TYPE          13       26             8        3
D40V20, multiclass
               clus
vv              DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  COMBINATION                              4                             13
  EXTERNAL                                11                             26
  EXTERNAL BEAM                            3                              8
  INTERNAL                                 2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V21, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED    1  2
  DEL PEAK 17(11P15.1) WILD-TYPE 10  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED      1    2
  DEL PEAK 17(11P15.1) WILD-TYPE   10    1
     clus
vv    DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  CGY                            1                             10
  GY                             2                              1
[1] 2 2
[1] FALSE
D40V22, continuous
D40V23, continuous
D40V24, continuous
D40V25, continuous
D40V26, continuous
D40V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 17(11P15.1) MUTATED                                     0
  DEL PEAK 17(11P15.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 17(11P15.1) MUTATED                                     2
  DEL PEAK 17(11P15.1) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 17(11P15.1) MUTATED                         2
  DEL PEAK 17(11P15.1) WILD-TYPE                       7
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 17(11P15.1) MUTATED                         1
  DEL PEAK 17(11P15.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 17(11P15.1) MUTATED                         1
  DEL PEAK 17(11P15.1) WILD-TYPE                       4
D40V28, multiclass
                                     clus
vv                                    DEL PEAK 17(11P15.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        2
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 17(11P15.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                          7
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 17(11P15.1) MUTATED                                               1
  DEL PEAK 17(11P15.1) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 17(11P15.1) MUTATED                                                6
  DEL PEAK 17(11P15.1) WILD-TYPE                                              4
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 17(11P15.1) MUTATED                                                                                  21
  DEL PEAK 17(11P15.1) WILD-TYPE                                                                                33
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 17(11P15.1) MUTATED                                                                                             18
  DEL PEAK 17(11P15.1) WILD-TYPE                                                                                           59
D40V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 17(11P15.1) 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)                                      21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           18
                                                                                              clus
vv                                                                                             DEL PEAK 17(11P15.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        33
  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"
D40V30, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   19 17
  DEL PEAK 17(11P15.1) WILD-TYPE 35 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     19   17
  DEL PEAK 17(11P15.1) WILD-TYPE   35   42
         clus
vv        DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  ABSENT                            19                             35
  PRESENT                           17                             42
[1] 2 2
[1] FALSE
D40V31, continuous
D40V32, continuous
D40V33, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   13 27
  DEL PEAK 17(11P15.1) WILD-TYPE 22 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     13   27
  DEL PEAK 17(11P15.1) WILD-TYPE   22   54
                                          clus
vv                                         DEL PEAK 17(11P15.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           27
                                          clus
vv                                         DEL PEAK 17(11P15.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             54
[1] 2 2
[1] FALSE
D40V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 17(11P15.1) MUTATED       1                   36                   2
  DEL PEAK 17(11P15.1) WILD-TYPE     2                   77                   3
D40V35, multiclass
                      clus
vv                     DEL PEAK 17(11P15.1) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           36
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     DEL PEAK 17(11P15.1) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             77
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 17(11P15.1) MUTATED              1          11         17
  DEL PEAK 17(11P15.1) WILD-TYPE            7          29         23
D40V36, multiclass
              clus
vv             DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  CURRENT USER                            1                              7
  FORMER USER                            11                             29
  NEVER USED                             17                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V37, continuous
D40V38, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.1) MUTATED   27  4
  DEL PEAK 17(11P15.1) WILD-TYPE 46 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.1) MUTATED     27    4
  DEL PEAK 17(11P15.1) WILD-TYPE   46   10
         clus
vv        DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  ABSENT                            27                             46
  PRESENT                            4                             10
[1] 2 2
[1] FALSE
D40V39, continuous
[1] "Remove cluster labels:"       "DEL PEAK 17(11P15.1) MUTATED"
clus
  DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1MN                     TCGA-C5-A1MP 
"DEL PEAK 17(11P15.1) WILD-TYPE" "DEL PEAK 17(11P15.1) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-HM-A3JK 
"DEL PEAK 17(11P15.1) WILD-TYPE" "DEL PEAK 17(11P15.1) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-MU-A51Y 
"DEL PEAK 17(11P15.1) WILD-TYPE" "DEL PEAK 17(11P15.1) WILD-TYPE" 
                    TCGA-MU-A8JM 
"DEL PEAK 17(11P15.1) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 17(11P15.1) MUTATED     1    0   8   18    4  1   1    2    3   4
  DEL PEAK 17(11P15.1) WILD-TYPE   1    1  14   33   17  2   5    4    5   9
                                vv
clus                             T3B T4 TX
  DEL PEAK 17(11P15.1) MUTATED     0  1  4
  DEL PEAK 17(11P15.1) WILD-TYPE   2  0  3
D40V40, multiclass
      clus
vv     DEL PEAK 17(11P15.1) MUTATED DEL PEAK 17(11P15.1) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             8                             14
  T1B1                           18                             33
  T1B2                            4                             17
  T2                              1                              2
  T2A                             1                              5
  T2A1                            2                              4
  T2A2                            3                              5
  T2B                             4                              9
  T3B                             0                              2
  T4                              1                              0
  TX                              4                              3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V41, continuous

Clustering(41) Variable = DEL PEAK 18(11Q25) MUTATION ANALYSIS
D41V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 18(11Q25) MUTATED   75 23
  DEL PEAK 18(11Q25) WILD-TYPE 62  9
  DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE 
                          98                           71 
  DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE 
                          23                            9 
$`DEL PEAK 18(11Q25) MUTATED`
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-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-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       31.40        46.32        30.21        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       35.61         0.46         2.43        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL 
      100.14         0.82        52.01       182.93        25.35        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL 
        9.67        17.19        60.69        13.61         2.73        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A411 
        8.28        12.36         1.32        13.05         1.18         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.50         1.81         0.26        13.91        14.99        14.96 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RD TCGA-EK-A2RL 
       13.48        12.59         6.64         0.53         0.03        23.70 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L 
        2.24         0.07         0.10        20.35         6.94         4.47 
TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        6.12        23.84         0.66         1.45         1.58         0.82 
TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
       21.67       137.16        66.81       117.40        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 
       26.56        36.36        20.48         0.10         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       13.87         0.03        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-R2-A69V TCGA-RA-A741 
        3.45         3.39         5.75         4.80        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

$`DEL PEAK 18(11Q25) WILD-TYPE`
TCGA-C5-A1BI TCGA-C5-A1BQ TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       36.56        19.86        35.01        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
       73.18        38.43        18.02        17.85        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZM 
      134.33        73.41        85.55        94.95         9.34        58.88 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       16.18         7.33         0.76         1.74         0.82         0.62 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO 
       14.50         1.35        12.66        12.82        14.89         1.48 
TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
        0.69        13.58        45.96         0.59         0.07         4.04 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RN 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-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TX 
       14.70         1.22         0.92         2.17         1.02         1.48 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         1.12        25.41 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-JW-A5VG 
       20.78        14.93         4.11       147.39        96.95        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AW 
       16.64        19.33        15.58        10.06         5.13         0.89 
TCGA-MU-A8JM TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73R 
        5.42         3.72         5.85         3.72         6.25 

  DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE 
                        0.03                         0.03 
  DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE 
                      182.93                       147.39 
  DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE 
                      14.975                        7.920 
[1] "0.0 - 182.9 (15.0)" "0.0 - 147.4 (7.9)" 
[1] "hr=" "1.3"
D41V2, continuous
                              vv
clus                           T1 T2+T3+T4
  DEL PEAK 18(11Q25) MUTATED   56       21
  DEL PEAK 18(11Q25) WILD-TYPE 41       18
D41V3, multiclass
          clus
vv         DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  T1                               56                           41
  T2+T3+T4                         21                           18
[1] 2 2
[1] FALSE
D41V4, binary
                              cls
clus                            0  1
  DEL PEAK 18(11Q25) MUTATED   50 24
  DEL PEAK 18(11Q25) WILD-TYPE 37 16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q25) MUTATED     50   24
  DEL PEAK 18(11Q25) WILD-TYPE   37   16
   clus
vv  DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  0                         50                           37
  1                         24                           16
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  DEL PEAK 18(11Q25) MUTATED   45  1 34
  DEL PEAK 18(11Q25) WILD-TYPE 27  2 31
D41V5, multiclass
    clus
vv   DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  M0                         45                           27
  M1                          1                            2
  MX                         34                           31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(11Q25) MUTATED               0                               91
  DEL PEAK 18(11Q25) WILD-TYPE             2                               53
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 18(11Q25) MUTATED                                               1
  DEL PEAK 18(11Q25) WILD-TYPE                                             3
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 18(11Q25) MUTATED                                     7
  DEL PEAK 18(11Q25) WILD-TYPE                                  13
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 18(11Q25) MUTATED                                           1
  DEL PEAK 18(11Q25) WILD-TYPE                                         1
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 18(11Q25) MUTATED                                              1
  DEL PEAK 18(11Q25) WILD-TYPE                                            3
D41V6, multiclass
                                               clus
vv                                              DEL PEAK 18(11Q25) MUTATED
  ADENOSQUAMOUS                                                          0
  CERVICAL SQUAMOUS CELL CARCINOMA                                      91
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           1
                                               clus
vv                                              DEL PEAK 18(11Q25) WILD-TYPE
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        53
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     13
  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"
D41V7, binary
                              cls
clus                            0  1
  DEL PEAK 18(11Q25) MUTATED   19 82
  DEL PEAK 18(11Q25) WILD-TYPE  8 67
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q25) MUTATED     19   82
  DEL PEAK 18(11Q25) WILD-TYPE    8   67
     clus
vv    DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  NO                          19                            8
  YES                         82                           67
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(11Q25) MUTATED                                  3    10
  DEL PEAK 18(11Q25) WILD-TYPE                                4     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(11Q25) MUTATED                          15
  DEL PEAK 18(11Q25) WILD-TYPE                         3
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(11Q25) MUTATED                                           1    70
  DEL PEAK 18(11Q25) WILD-TYPE                                         0    60
D41V10, multiclass
                                           clus
vv                                          DEL PEAK 18(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   3
  ASIAN                                                             10
  BLACK OR AFRICAN AMERICAN                                         15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             70
                                           clus
vv                                          DEL PEAK 18(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               60
[1] 5 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
  DEL PEAK 18(11Q25) MUTATED    3 72
  DEL PEAK 18(11Q25) WILD-TYPE  8 55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q25) MUTATED      3   72
  DEL PEAK 18(11Q25) WILD-TYPE    8   55
                        clus
vv                       DEL PEAK 18(11Q25) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         72
                        clus
vv                       DEL PEAK 18(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           55
[1] 2 2
[1] FALSE
D41V12, continuous
D41V13, binary
                              cls
clus                            0  1
  DEL PEAK 18(11Q25) MUTATED   33 15
  DEL PEAK 18(11Q25) WILD-TYPE 15  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q25) MUTATED     33   15
  DEL PEAK 18(11Q25) WILD-TYPE   15    4
            clus
vv           DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  TUMOR FREE                         33                           15
  WITH TUMOR                         15                            4
[1] 2 2
[1] FALSE
                              vv
clus                           NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 18(11Q25) MUTATED         1      4       2            86       8
  DEL PEAK 18(11Q25) WILD-TYPE       0      6       4            61       4
D41V14, multiclass
               clus
vv              DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  NIGERIA                                1                            0
  RUSSIA                                 4                            6
  UKRAINE                                2                            4
  UNITED STATES                         86                           61
  VIETNAM                                8                            4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           G1 G2 G3 G4 GX
  DEL PEAK 18(11Q25) MUTATED    6 48 43  1  3
  DEL PEAK 18(11Q25) WILD-TYPE  8 35 29  0  2
D41V15, multiclass
    clus
vv   DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  G1                          6                            8
  G2                         48                           35
  G3                         43                           29
  G4                          1                            0
  GX                          3                            2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V16, continuous
D41V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 18(11Q25) MUTATED                                            15
  DEL PEAK 18(11Q25) WILD-TYPE                                           6
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 18(11Q25) MUTATED                                        6
  DEL PEAK 18(11Q25) WILD-TYPE                                      2
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 18(11Q25) MUTATED                                                 0
  DEL PEAK 18(11Q25) WILD-TYPE                                               1
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 18(11Q25) MUTATED               17                  47
  DEL PEAK 18(11Q25) WILD-TYPE             19                  36
D41V18, multiclass
                                                 clus
vv                                                DEL PEAK 18(11Q25) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                             15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          0
  CURRENT SMOKER                                                          17
  LIFELONG NON-SMOKER                                                     47
                                                 clus
vv                                                DEL PEAK 18(11Q25) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            19
  LIFELONG NON-SMOKER                                                       36
[1] 5 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
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 18(11Q25) MUTATED            14       20             6        4
  DEL PEAK 18(11Q25) WILD-TYPE           3       17             5        1
D41V20, multiclass
               clus
vv              DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  COMBINATION                           14                            3
  EXTERNAL                              20                           17
  EXTERNAL BEAM                          6                            5
  INTERNAL                               4                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V21, binary
                              cls
clus                           0 1
  DEL PEAK 18(11Q25) MUTATED   6 3
  DEL PEAK 18(11Q25) WILD-TYPE 5 0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q25) MUTATED      6    3
  DEL PEAK 18(11Q25) WILD-TYPE    5    0
     clus
vv    DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  CGY                          6                            5
  GY                           3                            0
[1] 2 2
[1] FALSE
D41V22, continuous
D41V23, continuous
D41V24, continuous
D41V25, continuous
D41V26, continuous
D41V27, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 18(11Q25) MUTATED                                     1
  DEL PEAK 18(11Q25) WILD-TYPE                                   1
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 18(11Q25) MUTATED                                     5
  DEL PEAK 18(11Q25) WILD-TYPE                                   1
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 18(11Q25) MUTATED                         6                       1
  DEL PEAK 18(11Q25) WILD-TYPE                       3                       0
                              vv
clus                           POSITIVE VAGINAL MARGIN
  DEL PEAK 18(11Q25) MUTATED                         4
  DEL PEAK 18(11Q25) WILD-TYPE                       1
D41V28, multiclass
                                     clus
vv                                    DEL PEAK 18(11Q25) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          5
  OTHER LOCATION, SPECIFY                                      6
  POSITIVE BLADDER MARGIN                                      1
  POSITIVE VAGINAL MARGIN                                      4
                                     clus
vv                                    DEL PEAK 18(11Q25) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        3
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  DEL PEAK 18(11Q25) MUTATED                                               2
  DEL PEAK 18(11Q25) WILD-TYPE                                             0
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 18(11Q25) MUTATED                                                7
  DEL PEAK 18(11Q25) WILD-TYPE                                              3
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 18(11Q25) MUTATED                                                                                  37
  DEL PEAK 18(11Q25) WILD-TYPE                                                                                17
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 18(11Q25) MUTATED                                                                                             38
  DEL PEAK 18(11Q25) WILD-TYPE                                                                                           39
D41V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 18(11Q25) MUTATED
  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)                                    37
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         38
                                                                                              clus
vv                                                                                             DEL PEAK 18(11Q25) WILD-TYPE
  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)                                      17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V30, binary
                              cls
clus                            0  1
  DEL PEAK 18(11Q25) MUTATED   28 40
  DEL PEAK 18(11Q25) WILD-TYPE 26 19
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q25) MUTATED     28   40
  DEL PEAK 18(11Q25) WILD-TYPE   26   19
         clus
vv        DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  ABSENT                          28                           26
  PRESENT                         40                           19
[1] 2 2
[1] FALSE
D41V31, continuous
D41V32, continuous
D41V33, binary
                              cls
clus                            0  1
  DEL PEAK 18(11Q25) MUTATED   22 48
  DEL PEAK 18(11Q25) WILD-TYPE 13 33
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q25) MUTATED     22   48
  DEL PEAK 18(11Q25) WILD-TYPE   13   33
                                          clus
vv                                         DEL PEAK 18(11Q25) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         48
                                          clus
vv                                         DEL PEAK 18(11Q25) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           33
[1] 2 2
[1] FALSE
D41V34, continuous
                              vv
clus                           OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 18(11Q25) MUTATED       2                   64                   3
  DEL PEAK 18(11Q25) WILD-TYPE     1                   49                   2
D41V35, multiclass
                      clus
vv                     DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  OTHER                                         2                            1
  RADICAL HYSTERECTOMY                         64                           49
  SIMPLE HYSTERECTOMY                           3                            2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  DEL PEAK 18(11Q25) MUTATED              2          24         24
  DEL PEAK 18(11Q25) WILD-TYPE            6          16         16
D41V36, multiclass
              clus
vv             DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  CURRENT USER                          2                            6
  FORMER USER                          24                           16
  NEVER USED                           24                           16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V37, continuous
D41V38, binary
                              cls
clus                            0  1
  DEL PEAK 18(11Q25) MUTATED   42 11
  DEL PEAK 18(11Q25) WILD-TYPE 31  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q25) MUTATED     42   11
  DEL PEAK 18(11Q25) WILD-TYPE   31    3
         clus
vv        DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  ABSENT                          42                           31
  PRESENT                         11                            3
[1] 2 2
[1] FALSE
D41V39, continuous
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 18(11Q25) MUTATED     1    1  15   32    7  3   2    5    3   6   1
  DEL PEAK 18(11Q25) WILD-TYPE   1    0   7   19   14  0   4    1    5   7   1
                              vv
clus                           T4 TX
  DEL PEAK 18(11Q25) MUTATED    1  4
  DEL PEAK 18(11Q25) WILD-TYPE  0  3
D41V40, multiclass
      clus
vv     DEL PEAK 18(11Q25) MUTATED DEL PEAK 18(11Q25) WILD-TYPE
  T1A                           1                            1
  T1A1                          1                            0
  T1B                          15                            7
  T1B1                         32                           19
  T1B2                          7                           14
  T2                            3                            0
  T2A                           2                            4
  T2A1                          5                            1
  T2A2                          3                            5
  T2B                           6                            7
  T3B                           1                            1
  T4                            1                            0
  TX                            4                            3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V41, continuous

Clustering(42) Variable = DEL PEAK 19(13Q12.11) MUTATION ANALYSIS
D42V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 19(13Q12.11) MUTATED   44 11
  DEL PEAK 19(13Q12.11) WILD-TYPE 93 21
  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE 
                             55                             114 
  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE 
                             11                              21 
$`DEL PEAK 19(13Q12.11) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BL 
       49.48        57.04        68.84        18.74       144.16       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A2LV 
       82.85         5.46        31.40        38.99        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK 
       83.05        38.43        18.02       182.93        25.35       134.33 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZL 
       73.41        85.55        60.69        94.95         9.34        87.75 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A5ZD 
      117.99       118.65        12.36         1.18        12.66         0.69 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2R7 TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RM 
       12.59        45.96         0.59         4.04         0.36         2.24 
TCGA-EX-A1H5 TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A5XV 
       20.35         6.12        23.84         1.45         1.58         1.97 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JW-A5VK 
       25.41        21.67         4.11       147.39        78.71        20.48 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73R 
        0.10         0.89         0.07         5.85         3.39         6.25 
TCGA-R2-A69V 
       19.59 

$`DEL PEAK 19(13Q12.11) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BQ TCGA-C5-A1M5 
       23.67        11.44        36.56       177.04        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       46.32        30.21        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY 
        0.46         2.43        40.93         3.58        44.22        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
      100.14         0.82        52.01        17.85        20.42       101.82 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM 
       15.48         9.67        17.19        13.61         2.73        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       36.76         2.66        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28         0.76         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       13.05        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZE 
       12.82         0.26        14.89         1.48        13.91        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RB 
       14.96        13.58        13.48         6.64         0.53         0.07 
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-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.03         7.92         6.94        14.70         4.47 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX 
        1.22         0.92         2.17         0.66         1.02         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A3JK 
        0.82         3.52         1.35         1.32         1.12        20.78 
TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
       14.93       137.16        66.81       117.40        96.95        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       26.56        36.36        14.43        16.64        19.33        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       10.06         5.13         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         2.96         3.72         3.45 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.72         5.75         4.80         3.88        11.67        93.99 

  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE 
                         182.93                          177.04 
  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE 
                          21.67                           10.75 
[1] "0.1 - 182.9 (21.7)" "0.0 - 177.0 (10.8)"
[1] "hr=" "1.9"
D42V2, continuous
                                 vv
clus                              T1 T2+T3+T4
  DEL PEAK 19(13Q12.11) MUTATED   28       11
  DEL PEAK 19(13Q12.11) WILD-TYPE 69       28
D42V3, multiclass
          clus
vv         DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  T1                                  28                              69
  T2+T3+T4                            11                              28
[1] 2 2
[1] FALSE
D42V4, binary
                                 cls
clus                               0  1
  DEL PEAK 19(13Q12.11) MUTATED   24 15
  DEL PEAK 19(13Q12.11) WILD-TYPE 63 25
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(13Q12.11) MUTATED     24   15
  DEL PEAK 19(13Q12.11) WILD-TYPE   63   25
   clus
vv  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  0                            24                              63
  1                            15                              25
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 19(13Q12.11) MUTATED   22  1 20
  DEL PEAK 19(13Q12.11) WILD-TYPE 50  2 45
D42V5, multiclass
    clus
vv   DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  M0                            22                              50
  M1                             1                               2
  MX                            20                              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 19(13Q12.11) MUTATED               1
  DEL PEAK 19(13Q12.11) WILD-TYPE             1
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(13Q12.11) MUTATED                                 58
  DEL PEAK 19(13Q12.11) WILD-TYPE                               86
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 19(13Q12.11) MUTATED                                               0
  DEL PEAK 19(13Q12.11) WILD-TYPE                                             4
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 19(13Q12.11) MUTATED                                     2
  DEL PEAK 19(13Q12.11) WILD-TYPE                                  18
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 19(13Q12.11) MUTATED                                           0
  DEL PEAK 19(13Q12.11) WILD-TYPE                                         2
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 19(13Q12.11) MUTATED                                              0
  DEL PEAK 19(13Q12.11) WILD-TYPE                                            4
D42V6, multiclass
                                               clus
vv                                              DEL PEAK 19(13Q12.11) MUTATED
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         58
  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                                              DEL PEAK 19(13Q12.11) WILD-TYPE
  ADENOSQUAMOUS                                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                                           86
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                                 cls
clus                                0   1
  DEL PEAK 19(13Q12.11) MUTATED    13  48
  DEL PEAK 19(13Q12.11) WILD-TYPE  14 101
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(13Q12.11) MUTATED     13   48
  DEL PEAK 19(13Q12.11) WILD-TYPE   14  101
     clus
vv    DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  NO                             13                              14
  YES                            48                             101
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(13Q12.11) MUTATED                                  0     6
  DEL PEAK 19(13Q12.11) WILD-TYPE                                7     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(13Q12.11) MUTATED                           9
  DEL PEAK 19(13Q12.11) WILD-TYPE                         9
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 19(13Q12.11) MUTATED                                           0
  DEL PEAK 19(13Q12.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 19(13Q12.11) MUTATED      45
  DEL PEAK 19(13Q12.11) WILD-TYPE    85
D42V10, multiclass
                                           clus
vv                                          DEL PEAK 19(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                45
                                           clus
vv                                          DEL PEAK 19(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                   9
  BLACK OR AFRICAN AMERICAN                                               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                  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"
D42V11, binary
                                 cls
clus                               0  1
  DEL PEAK 19(13Q12.11) MUTATED    0 44
  DEL PEAK 19(13Q12.11) WILD-TYPE 11 83
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(13Q12.11) MUTATED      0   44
  DEL PEAK 19(13Q12.11) WILD-TYPE   11   83
                        clus
vv                       DEL PEAK 19(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            44
                        clus
vv                       DEL PEAK 19(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                              83
[1] 2 2
[1] FALSE
D42V12, continuous
D42V13, binary
                                 cls
clus                               0  1
  DEL PEAK 19(13Q12.11) MUTATED   17  6
  DEL PEAK 19(13Q12.11) WILD-TYPE 31 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(13Q12.11) MUTATED     17    6
  DEL PEAK 19(13Q12.11) WILD-TYPE   31   13
            clus
vv           DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  TUMOR FREE                            17                              31
  WITH TUMOR                             6                              13
[1] 2 2
[1] FALSE
                                 vv
clus                              NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 19(13Q12.11) MUTATED         0      2       1            53       5
  DEL PEAK 19(13Q12.11) WILD-TYPE       1      8       5            94       7
D42V14, multiclass
               clus
vv              DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  NIGERIA                                   0                               1
  RUSSIA                                    2                               8
  UKRAINE                                   1                               5
  UNITED STATES                            53                              94
  VIETNAM                                   5                               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 19(13Q12.11) MUTATED    2 25 30  1  2
  DEL PEAK 19(13Q12.11) WILD-TYPE 12 58 42  0  3
D42V15, multiclass
    clus
vv   DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  G1                             2                              12
  G2                            25                              58
  G3                            30                              42
  G4                             1                               0
  GX                             2                               3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V16, continuous
D42V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 19(13Q12.11) MUTATED                                             7
  DEL PEAK 19(13Q12.11) WILD-TYPE                                          14
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 19(13Q12.11) MUTATED                                        4
  DEL PEAK 19(13Q12.11) WILD-TYPE                                      4
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 19(13Q12.11) MUTATED                                                 1
  DEL PEAK 19(13Q12.11) WILD-TYPE                                               0
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 19(13Q12.11) MUTATED               14                  23
  DEL PEAK 19(13Q12.11) WILD-TYPE             22                  60
D42V18, multiclass
                                                 clus
vv                                                DEL PEAK 19(13Q12.11) 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                                                        23
                                                 clus
vv                                                DEL PEAK 19(13Q12.11) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               0
  CURRENT SMOKER                                                               22
  LIFELONG NON-SMOKER                                                          60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V19, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 19(13Q12.11) MUTATED             9       11             3        2
  DEL PEAK 19(13Q12.11) WILD-TYPE           8       26             8        3
D42V20, multiclass
               clus
vv              DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  COMBINATION                               9                               8
  EXTERNAL                                 11                              26
  EXTERNAL BEAM                             3                               8
  INTERNAL                                  2                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V21, binary
                                 cls
clus                              0 1
  DEL PEAK 19(13Q12.11) MUTATED   4 1
  DEL PEAK 19(13Q12.11) WILD-TYPE 7 2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(13Q12.11) MUTATED      4    1
  DEL PEAK 19(13Q12.11) WILD-TYPE    7    2
     clus
vv    DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  CGY                             4                               7
  GY                              1                               2
[1] 2 2
[1] FALSE
D42V22, continuous
D42V23, continuous
D42V24, continuous
D42V25, continuous
D42V26, continuous
D42V27, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 19(13Q12.11) MUTATED                                     0
  DEL PEAK 19(13Q12.11) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 19(13Q12.11) MUTATED                                     1
  DEL PEAK 19(13Q12.11) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 19(13Q12.11) MUTATED                         3
  DEL PEAK 19(13Q12.11) WILD-TYPE                       6
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 19(13Q12.11) MUTATED                         0
  DEL PEAK 19(13Q12.11) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 19(13Q12.11) MUTATED                         3
  DEL PEAK 19(13Q12.11) WILD-TYPE                       2
D42V28, multiclass
                                     clus
vv                                    DEL PEAK 19(13Q12.11) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         3
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         3
                                     clus
vv                                    DEL PEAK 19(13Q12.11) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                           6
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           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)
  DEL PEAK 19(13Q12.11) MUTATED                                               0
  DEL PEAK 19(13Q12.11) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 19(13Q12.11) MUTATED                                                3
  DEL PEAK 19(13Q12.11) WILD-TYPE                                              7
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 19(13Q12.11) MUTATED                                                                                  19
  DEL PEAK 19(13Q12.11) WILD-TYPE                                                                                35
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 19(13Q12.11) MUTATED                                                                                             24
  DEL PEAK 19(13Q12.11) WILD-TYPE                                                                                           53
D42V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 19(13Q12.11) 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)                                       19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            24
                                                                                              clus
vv                                                                                             DEL PEAK 19(13Q12.11) 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)                                         35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V30, binary
                                 cls
clus                               0  1
  DEL PEAK 19(13Q12.11) MUTATED   13 20
  DEL PEAK 19(13Q12.11) WILD-TYPE 41 39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(13Q12.11) MUTATED     13   20
  DEL PEAK 19(13Q12.11) WILD-TYPE   41   39
         clus
vv        DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  ABSENT                             13                              41
  PRESENT                            20                              39
[1] 2 2
[1] FALSE
D42V31, continuous
D42V32, continuous
D42V33, binary
                                 cls
clus                               0  1
  DEL PEAK 19(13Q12.11) MUTATED   12 31
  DEL PEAK 19(13Q12.11) WILD-TYPE 23 50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(13Q12.11) MUTATED     12   31
  DEL PEAK 19(13Q12.11) WILD-TYPE   23   50
                                          clus
vv                                         DEL PEAK 19(13Q12.11) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            31
                                          clus
vv                                         DEL PEAK 19(13Q12.11) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              50
[1] 2 2
[1] FALSE
D42V34, continuous
                                 vv
clus                              OTHER RADICAL HYSTERECTOMY
  DEL PEAK 19(13Q12.11) MUTATED       0                   36
  DEL PEAK 19(13Q12.11) WILD-TYPE     3                   77
                                 vv
clus                              SIMPLE HYSTERECTOMY
  DEL PEAK 19(13Q12.11) MUTATED                     2
  DEL PEAK 19(13Q12.11) WILD-TYPE                   3
D42V35, multiclass
                      clus
vv                     DEL PEAK 19(13Q12.11) MUTATED
  OTHER                                            0
  RADICAL HYSTERECTOMY                            36
  SIMPLE HYSTERECTOMY                              2
                      clus
vv                     DEL PEAK 19(13Q12.11) WILD-TYPE
  OTHER                                              3
  RADICAL HYSTERECTOMY                              77
  SIMPLE HYSTERECTOMY                                3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 19(13Q12.11) MUTATED              2          11         12
  DEL PEAK 19(13Q12.11) WILD-TYPE            6          29         28
D42V36, multiclass
              clus
vv             DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  CURRENT USER                             2                               6
  FORMER USER                             11                              29
  NEVER USED                              12                              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V37, continuous
D42V38, binary
                                 cls
clus                               0  1
  DEL PEAK 19(13Q12.11) MUTATED   17  6
  DEL PEAK 19(13Q12.11) WILD-TYPE 56  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(13Q12.11) MUTATED     17    6
  DEL PEAK 19(13Q12.11) WILD-TYPE   56    8
         clus
vv        DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  ABSENT                             17                              56
  PRESENT                             6                               8
[1] 2 2
[1] FALSE
D42V39, continuous
[1] "Remove cluster labels:"        "DEL PEAK 19(13Q12.11) MUTATED"
clus
  DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE 
                              2                               7 
                     TCGA-C5-A1MN                      TCGA-C5-A1MP 
"DEL PEAK 19(13Q12.11) WILD-TYPE" "DEL PEAK 19(13Q12.11) WILD-TYPE" 
                     TCGA-EK-A2RO                      TCGA-HM-A3JK 
"DEL PEAK 19(13Q12.11) WILD-TYPE" "DEL PEAK 19(13Q12.11) WILD-TYPE" 
                     TCGA-JW-A852                      TCGA-MU-A51Y 
"DEL PEAK 19(13Q12.11) WILD-TYPE" "DEL PEAK 19(13Q12.11) WILD-TYPE" 
                     TCGA-MU-A8JM 
"DEL PEAK 19(13Q12.11) WILD-TYPE" 
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 19(13Q12.11) MUTATED     1    0   9   12    6  3   1    2    2   3
  DEL PEAK 19(13Q12.11) WILD-TYPE   1    1  13   39   15  0   5    4    6  10
                                 vv
clus                              T3B T4 TX
  DEL PEAK 19(13Q12.11) MUTATED     0  0  4
  DEL PEAK 19(13Q12.11) WILD-TYPE   2  1  3
D42V40, multiclass
      clus
vv     DEL PEAK 19(13Q12.11) MUTATED DEL PEAK 19(13Q12.11) WILD-TYPE
  T1A                              1                               1
  T1A1                             0                               1
  T1B                              9                              13
  T1B1                            12                              39
  T1B2                             6                              15
  T2                               3                               0
  T2A                              1                               5
  T2A1                             2                               4
  T2A2                             2                               6
  T2B                              3                              10
  T3B                              0                               2
  T4                               0                               1
  TX                               4                               3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V41, continuous

Clustering(43) Variable = DEL PEAK 20(13Q14.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(13Q14.2) MUTATED   51 10
  DEL PEAK 20(13Q14.2) WILD-TYPE 86 22
  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE 
                            61                            108 
  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE 
                            10                             22 
$`DEL PEAK 20(13Q14.2) MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BL 
       49.48        57.04        68.84        18.74       144.16       173.29 
TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A2LV 
       82.85        31.40        57.73        38.99        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK 
       83.05        38.43        18.02       182.93        25.35       134.33 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZL 
       73.41        85.55        60.69        94.95         9.34        87.75 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3QD TCGA-EA-A3QE 
      117.99       118.65        22.98        12.36        13.05         1.18 
TCGA-EA-A439 TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 
       14.50        13.48        12.59        45.96         0.53         0.59 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A69M TCGA-FU-A23L 
        0.03         0.36         0.10        20.35         6.12        23.84 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.45         1.58         1.48         1.97        25.41        21.67 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A852 
       14.93         4.11       147.39        78.71        20.48         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MY-A5BE TCGA-Q1-A6DT TCGA-Q1-A73R 
        0.10         0.89         0.07         0.07         3.39         6.25 
TCGA-R2-A69V 
       19.59 

$`DEL PEAK 20(13Q14.2) WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1BQ 
       23.67        11.44        36.56       177.04         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI 
       67.46        46.32        30.21        35.01        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY 
        0.46         2.43        40.93         3.58        44.22        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
      100.14         0.82        52.01        17.85        20.42       101.82 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM 
       15.48         9.67        17.19        13.61         2.73        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       36.76         2.66        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3Y4 
        0.76         1.74         1.32         0.82         0.62        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RL 
       13.58         6.64         0.07         4.04         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
        2.24         0.10         0.07         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        6.94        14.70         4.47         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        0.66         1.02         0.82         3.52         1.35         1.32 
TCGA-FU-A770 TCGA-HM-A3JK TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        1.12        20.78       137.16        66.81       117.40        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       15.58        10.06         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       29.72         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.72         5.75         4.80         3.88        11.67        93.99 

  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE 
                        182.93                         177.04 
  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE 
                        20.480                          8.975 
[1] "0.0 - 182.9 (20.5)" "0.0 - 177.0 (9.0)" 
[1] "hr=" "2.4"
D43V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 20(13Q14.2) MUTATED   35       13
  DEL PEAK 20(13Q14.2) WILD-TYPE 62       26
D43V3, multiclass
          clus
vv         DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  T1                                 35                             62
  T2+T3+T4                           13                             26
[1] 2 2
[1] FALSE
D43V4, binary
                                cls
clus                              0  1
  DEL PEAK 20(13Q14.2) MUTATED   29 18
  DEL PEAK 20(13Q14.2) WILD-TYPE 58 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q14.2) MUTATED     29   18
  DEL PEAK 20(13Q14.2) WILD-TYPE   58   22
   clus
vv  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  0                           29                             58
  1                           18                             22
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 20(13Q14.2) MUTATED   26  1 23
  DEL PEAK 20(13Q14.2) WILD-TYPE 46  2 42
D43V5, multiclass
    clus
vv   DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  M0                           26                             46
  M1                            1                              2
  MX                           23                             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"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(13Q14.2) MUTATED               1                               63
  DEL PEAK 20(13Q14.2) WILD-TYPE             1                               81
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 20(13Q14.2) MUTATED                                               0
  DEL PEAK 20(13Q14.2) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 20(13Q14.2) MUTATED                                     3
  DEL PEAK 20(13Q14.2) WILD-TYPE                                  17
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 20(13Q14.2) MUTATED                                           0
  DEL PEAK 20(13Q14.2) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 20(13Q14.2) MUTATED                                              0
  DEL PEAK 20(13Q14.2) WILD-TYPE                                            4
D43V6, multiclass
                                               clus
vv                                              DEL PEAK 20(13Q14.2) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        63
  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                                              DEL PEAK 20(13Q14.2) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                          81
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(13Q14.2) MUTATED   13 54
  DEL PEAK 20(13Q14.2) WILD-TYPE 14 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q14.2) MUTATED     13   54
  DEL PEAK 20(13Q14.2) WILD-TYPE   14   95
     clus
vv    DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  NO                            13                             14
  YES                           54                             95
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(13Q14.2) MUTATED                                  1     7
  DEL PEAK 20(13Q14.2) WILD-TYPE                                6     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(13Q14.2) MUTATED                          11
  DEL PEAK 20(13Q14.2) WILD-TYPE                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 20(13Q14.2) MUTATED                                           1
  DEL PEAK 20(13Q14.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 20(13Q14.2) MUTATED      45
  DEL PEAK 20(13Q14.2) WILD-TYPE    85
D43V10, multiclass
                                           clus
vv                                          DEL PEAK 20(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               45
                                           clus
vv                                          DEL PEAK 20(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                  8
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"
D43V11, binary
                                cls
clus                              0  1
  DEL PEAK 20(13Q14.2) MUTATED    1 46
  DEL PEAK 20(13Q14.2) WILD-TYPE 10 81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q14.2) MUTATED      1   46
  DEL PEAK 20(13Q14.2) WILD-TYPE   10   81
                        clus
vv                       DEL PEAK 20(13Q14.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           46
                        clus
vv                       DEL PEAK 20(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             81
[1] 2 2
[1] FALSE
D43V12, continuous
D43V13, binary
                                cls
clus                              0  1
  DEL PEAK 20(13Q14.2) MUTATED   22  5
  DEL PEAK 20(13Q14.2) WILD-TYPE 26 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q14.2) MUTATED     22    5
  DEL PEAK 20(13Q14.2) WILD-TYPE   26   14
            clus
vv           DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  TUMOR FREE                           22                             26
  WITH TUMOR                            5                             14
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 20(13Q14.2) MUTATED         0      2       0            59       6
  DEL PEAK 20(13Q14.2) WILD-TYPE       1      8       6            88       6
D43V14, multiclass
               clus
vv              DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  0                              6
  UNITED STATES                           59                             88
  VIETNAM                                  6                              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                             G1 G2 G3 G4 GX
  DEL PEAK 20(13Q14.2) MUTATED    3 25 35  1  2
  DEL PEAK 20(13Q14.2) WILD-TYPE 11 58 37  0  3
D43V15, multiclass
    clus
vv   DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  G1                            3                             11
  G2                           25                             58
  G3                           35                             37
  G4                            1                              0
  GX                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V16, continuous
D43V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 20(13Q14.2) MUTATED                                             9
  DEL PEAK 20(13Q14.2) WILD-TYPE                                          12
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 20(13Q14.2) MUTATED                                        6
  DEL PEAK 20(13Q14.2) WILD-TYPE                                      2
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 20(13Q14.2) MUTATED                                                 1
  DEL PEAK 20(13Q14.2) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 20(13Q14.2) MUTATED               13                  25
  DEL PEAK 20(13Q14.2) WILD-TYPE             23                  58
D43V18, multiclass
                                                 clus
vv                                                DEL PEAK 20(13Q14.2) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            13
  LIFELONG NON-SMOKER                                                       25
                                                 clus
vv                                                DEL PEAK 20(13Q14.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                              23
  LIFELONG NON-SMOKER                                                         58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 20(13Q14.2) MUTATED             8       11             4        2
  DEL PEAK 20(13Q14.2) WILD-TYPE           9       26             7        3
D43V20, multiclass
               clus
vv              DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  COMBINATION                              8                              9
  EXTERNAL                                11                             26
  EXTERNAL BEAM                            4                              7
  INTERNAL                                 2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V21, binary
                                cls
clus                             0 1
  DEL PEAK 20(13Q14.2) MUTATED   5 1
  DEL PEAK 20(13Q14.2) WILD-TYPE 6 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q14.2) MUTATED      5    1
  DEL PEAK 20(13Q14.2) WILD-TYPE    6    2
     clus
vv    DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  CGY                            5                              6
  GY                             1                              2
[1] 2 2
[1] FALSE
D43V22, continuous
D43V23, continuous
D43V24, continuous
D43V25, continuous
D43V26, continuous
D43V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 20(13Q14.2) MUTATED                                     0
  DEL PEAK 20(13Q14.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 20(13Q14.2) MUTATED                                     1
  DEL PEAK 20(13Q14.2) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 20(13Q14.2) MUTATED                         5
  DEL PEAK 20(13Q14.2) WILD-TYPE                       4
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 20(13Q14.2) MUTATED                         0
  DEL PEAK 20(13Q14.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 20(13Q14.2) MUTATED                         3
  DEL PEAK 20(13Q14.2) WILD-TYPE                       2
D43V28, multiclass
                                     clus
vv                                    DEL PEAK 20(13Q14.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        5
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        3
                                     clus
vv                                    DEL PEAK 20(13Q14.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          4
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 20(13Q14.2) MUTATED                                               0
  DEL PEAK 20(13Q14.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 20(13Q14.2) MUTATED                                                4
  DEL PEAK 20(13Q14.2) WILD-TYPE                                              6
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 20(13Q14.2) MUTATED                                                                                  23
  DEL PEAK 20(13Q14.2) WILD-TYPE                                                                                31
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 20(13Q14.2) MUTATED                                                                                             26
  DEL PEAK 20(13Q14.2) WILD-TYPE                                                                                           51
D43V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 20(13Q14.2) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           26
                                                                                              clus
vv                                                                                             DEL PEAK 20(13Q14.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        31
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V30, binary
                                cls
clus                              0  1
  DEL PEAK 20(13Q14.2) MUTATED   16 22
  DEL PEAK 20(13Q14.2) WILD-TYPE 38 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q14.2) MUTATED     16   22
  DEL PEAK 20(13Q14.2) WILD-TYPE   38   37
         clus
vv        DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  ABSENT                            16                             38
  PRESENT                           22                             37
[1] 2 2
[1] FALSE
D43V31, continuous
D43V32, continuous
D43V33, binary
                                cls
clus                              0  1
  DEL PEAK 20(13Q14.2) MUTATED   14 34
  DEL PEAK 20(13Q14.2) WILD-TYPE 21 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q14.2) MUTATED     14   34
  DEL PEAK 20(13Q14.2) WILD-TYPE   21   47
                                          clus
vv                                         DEL PEAK 20(13Q14.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               14
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           34
                                          clus
vv                                         DEL PEAK 20(13Q14.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             47
[1] 2 2
[1] FALSE
D43V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 20(13Q14.2) MUTATED       0                   41                   2
  DEL PEAK 20(13Q14.2) WILD-TYPE     3                   72                   3
D43V35, multiclass
                      clus
vv                     DEL PEAK 20(13Q14.2) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           41
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     DEL PEAK 20(13Q14.2) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             72
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 20(13Q14.2) MUTATED              2          14         10
  DEL PEAK 20(13Q14.2) WILD-TYPE            6          26         30
D43V36, multiclass
              clus
vv             DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                            14                             26
  NEVER USED                             10                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V37, continuous
D43V38, binary
                                cls
clus                              0  1
  DEL PEAK 20(13Q14.2) MUTATED   19  7
  DEL PEAK 20(13Q14.2) WILD-TYPE 54  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q14.2) MUTATED     19    7
  DEL PEAK 20(13Q14.2) WILD-TYPE   54    7
         clus
vv        DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  ABSENT                            19                             54
  PRESENT                            7                              7
[1] 2 2
[1] FALSE
D43V39, continuous
[1] "Remove cluster labels:"       "DEL PEAK 20(13Q14.2) MUTATED"
clus
  DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1BN                     TCGA-C5-A1MN 
"DEL PEAK 20(13Q14.2) WILD-TYPE" "DEL PEAK 20(13Q14.2) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK 20(13Q14.2) WILD-TYPE" "DEL PEAK 20(13Q14.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-MU-A51Y 
"DEL PEAK 20(13Q14.2) WILD-TYPE" "DEL PEAK 20(13Q14.2) WILD-TYPE" 
                    TCGA-MU-A8JM 
"DEL PEAK 20(13Q14.2) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 20(13Q14.2) MUTATED     1    0   9   17    8  3   1    3    1   4
  DEL PEAK 20(13Q14.2) WILD-TYPE   1    1  13   34   13  0   5    3    7   9
                                vv
clus                             T3B T4 TX
  DEL PEAK 20(13Q14.2) MUTATED     1  0  3
  DEL PEAK 20(13Q14.2) WILD-TYPE   1  1  4
D43V40, multiclass
      clus
vv     DEL PEAK 20(13Q14.2) MUTATED DEL PEAK 20(13Q14.2) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             9                             13
  T1B1                           17                             34
  T1B2                            8                             13
  T2                              3                              0
  T2A                             1                              5
  T2A1                            3                              3
  T2A2                            1                              7
  T2B                             4                              9
  T3B                             1                              1
  T4                              0                              1
  TX                              3                              4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V41, continuous

Clustering(44) Variable = DEL PEAK 21(14Q32.31) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 21(14Q32.31) MUTATED    23   1
  DEL PEAK 21(14Q32.31) WILD-TYPE 114  31
  DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE 
                             24                             145 
  DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE 
                              1                              31 
$`DEL PEAK 21(14Q32.31) MUTATED`
TCGA-BI-A20A TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A2LX TCGA-C5-A2M1 
       23.67        57.73        53.16         0.46        83.05        38.43 
TCGA-C5-A3HE TCGA-EA-A3HQ TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A78R 
       18.02         1.74        14.50         1.35         1.81        13.48 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-FU-A23L TCGA-FU-A3TX 
        0.53         0.59         1.18         2.24        23.84         1.48 
TCGA-IR-A3LA TCGA-IR-A3LH TCGA-LP-A4AU TCGA-MY-A5BD TCGA-Q1-A5R2 TCGA-Q1-A73R 
      137.16        78.71         0.10        29.72         3.45         6.25 

$`DEL PEAK 21(14Q32.31) 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-A1MH 
       67.46        31.40        46.32        30.21        35.01        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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF 
       73.45        78.35       100.14         0.82        52.01        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       182.93        25.35       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        9.34        13.61         2.73        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
        7.33         8.28         0.76        12.36         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A44S 
        0.62        13.05         1.18         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         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.99        14.96        13.58        12.59        45.96         6.64 
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-FU-A23K TCGA-FU-A2QG 
        6.94        14.70         4.47         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        2.17         0.66         1.02         1.45         1.58         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         1.12        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
       21.67        20.78        14.93         4.11       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        81.96        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       16.64        19.33        20.48        15.58        10.06         5.13 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.07         4.34         2.96         3.72         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        3.72         5.75         4.80        19.59         3.88        11.67 
TCGA-UC-A7PF 
       93.99 

  DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE 
                         137.16                          182.93 
  DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE 
                          9.865                          13.610 
[1] "0.1 - 137.2 (9.9)"  "0.0 - 182.9 (13.6)"
[1] "hr=" "4.5"
D44V2, continuous
                                 vv
clus                              T1 T2+T3+T4
  DEL PEAK 21(14Q32.31) MUTATED   14        6
  DEL PEAK 21(14Q32.31) WILD-TYPE 83       33
D44V3, multiclass
          clus
vv         DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  T1                                  14                              83
  T2+T3+T4                             6                              33
[1] 2 2
[1] FALSE
D44V4, binary
                                 cls
clus                               0  1
  DEL PEAK 21(14Q32.31) MUTATED   16  3
  DEL PEAK 21(14Q32.31) WILD-TYPE 71 37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.31) MUTATED     16    3
  DEL PEAK 21(14Q32.31) WILD-TYPE   71   37
   clus
vv  DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  0                            16                              71
  1                             3                              37
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 21(14Q32.31) MUTATED   14  0  8
  DEL PEAK 21(14Q32.31) WILD-TYPE 58  3 57
D44V5, multiclass
    clus
vv   DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  M0                            14                              58
  M1                             0                               3
  MX                             8                              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 21(14Q32.31) MUTATED               0
  DEL PEAK 21(14Q32.31) WILD-TYPE             2
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(14Q32.31) MUTATED                                 21
  DEL PEAK 21(14Q32.31) WILD-TYPE                              123
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 21(14Q32.31) MUTATED                                               0
  DEL PEAK 21(14Q32.31) WILD-TYPE                                             4
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 21(14Q32.31) MUTATED                                     5
  DEL PEAK 21(14Q32.31) WILD-TYPE                                  15
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 21(14Q32.31) MUTATED                                           1
  DEL PEAK 21(14Q32.31) WILD-TYPE                                         1
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 21(14Q32.31) MUTATED                                              0
  DEL PEAK 21(14Q32.31) WILD-TYPE                                            4
D44V6, multiclass
                                               clus
vv                                              DEL PEAK 21(14Q32.31) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         21
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              0
                                               clus
vv                                              DEL PEAK 21(14Q32.31) WILD-TYPE
  ADENOSQUAMOUS                                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   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"
D44V7, binary
                                 cls
clus                                0   1
  DEL PEAK 21(14Q32.31) MUTATED     2  25
  DEL PEAK 21(14Q32.31) WILD-TYPE  25 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.31) MUTATED      2   25
  DEL PEAK 21(14Q32.31) WILD-TYPE   25  124
     clus
vv    DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  NO                              2                              25
  YES                            25                             124
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(14Q32.31) MUTATED                                  0     2
  DEL PEAK 21(14Q32.31) WILD-TYPE                                7    13
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(14Q32.31) MUTATED                           2
  DEL PEAK 21(14Q32.31) WILD-TYPE                        16
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 21(14Q32.31) MUTATED                                           0
  DEL PEAK 21(14Q32.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 21(14Q32.31) MUTATED      22
  DEL PEAK 21(14Q32.31) WILD-TYPE   108
D44V10, multiclass
                                           clus
vv                                          DEL PEAK 21(14Q32.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 2
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                22
                                           clus
vv                                          DEL PEAK 21(14Q32.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        7
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 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"
D44V11, binary
                                 cls
clus                                0   1
  DEL PEAK 21(14Q32.31) MUTATED     2  17
  DEL PEAK 21(14Q32.31) WILD-TYPE   9 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.31) MUTATED      2   17
  DEL PEAK 21(14Q32.31) WILD-TYPE    9  110
                        clus
vv                       DEL PEAK 21(14Q32.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            17
                        clus
vv                       DEL PEAK 21(14Q32.31) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             110
[1] 2 2
[1] FALSE
D44V12, continuous
D44V13, binary
                                 cls
clus                               0  1
  DEL PEAK 21(14Q32.31) MUTATED   11  0
  DEL PEAK 21(14Q32.31) WILD-TYPE 37 19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.31) MUTATED     11    0
  DEL PEAK 21(14Q32.31) WILD-TYPE   37   19
            clus
vv           DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  TUMOR FREE                            11                              37
  WITH TUMOR                             0                              19
[1] 2 2
[1] FALSE
                                 vv
clus                              NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 21(14Q32.31) MUTATED         0      2       2            21       2
  DEL PEAK 21(14Q32.31) WILD-TYPE       1      8       4           126      10
D44V14, multiclass
               clus
vv              DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  NIGERIA                                   0                               1
  RUSSIA                                    2                               8
  UKRAINE                                   2                               4
  UNITED STATES                            21                             126
  VIETNAM                                   2                              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 21(14Q32.31) MUTATED    2  9 14  1  1
  DEL PEAK 21(14Q32.31) WILD-TYPE 12 74 58  0  4
D44V15, multiclass
    clus
vv   DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  G1                             2                              12
  G2                             9                              74
  G3                            14                              58
  G4                             1                               0
  GX                             1                               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V16, continuous
D44V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 21(14Q32.31) MUTATED                                             4
  DEL PEAK 21(14Q32.31) WILD-TYPE                                          17
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 21(14Q32.31) MUTATED                                        0
  DEL PEAK 21(14Q32.31) WILD-TYPE                                      8
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 21(14Q32.31) MUTATED                                                 0
  DEL PEAK 21(14Q32.31) WILD-TYPE                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 21(14Q32.31) MUTATED                1                  15
  DEL PEAK 21(14Q32.31) WILD-TYPE             35                  68
D44V18, multiclass
                                                 clus
vv                                                DEL PEAK 21(14Q32.31) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                              1
  LIFELONG NON-SMOKER                                                        15
                                                 clus
vv                                                DEL PEAK 21(14Q32.31) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               35
  LIFELONG NON-SMOKER                                                          68
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V19, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 21(14Q32.31) MUTATED             2        6             0        0
  DEL PEAK 21(14Q32.31) WILD-TYPE          15       31            11        5
D44V20, multiclass
               clus
vv              DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  COMBINATION                               2                              15
  EXTERNAL                                  6                              31
  EXTERNAL BEAM                             0                              11
  INTERNAL                                  0                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V21, binary
                                 cls
clus                              0 1
  DEL PEAK 21(14Q32.31) MUTATED   2 0
  DEL PEAK 21(14Q32.31) WILD-TYPE 9 3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.31) MUTATED      2    0
  DEL PEAK 21(14Q32.31) WILD-TYPE    9    3
     clus
vv    DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  CGY                             2                               9
  GY                              0                               3
[1] 2 2
[1] FALSE
D44V22, continuous
D44V23, continuous
D44V24, continuous
D44V25, continuous
D44V26, continuous
D44V27, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 21(14Q32.31) MUTATED                                     0
  DEL PEAK 21(14Q32.31) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 21(14Q32.31) MUTATED                                     1
  DEL PEAK 21(14Q32.31) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 21(14Q32.31) MUTATED                         0
  DEL PEAK 21(14Q32.31) WILD-TYPE                       9
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 21(14Q32.31) MUTATED                         0
  DEL PEAK 21(14Q32.31) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 21(14Q32.31) MUTATED                         2
  DEL PEAK 21(14Q32.31) WILD-TYPE                       3
D44V28, multiclass
                                     clus
vv                                    DEL PEAK 21(14Q32.31) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         0
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         2
                                     clus
vv                                    DEL PEAK 21(14Q32.31) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                           9
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           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)
  DEL PEAK 21(14Q32.31) MUTATED                                               0
  DEL PEAK 21(14Q32.31) WILD-TYPE                                             2
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 21(14Q32.31) MUTATED                                                1
  DEL PEAK 21(14Q32.31) WILD-TYPE                                              9
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 21(14Q32.31) MUTATED                                                                                  12
  DEL PEAK 21(14Q32.31) WILD-TYPE                                                                                42
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 21(14Q32.31) MUTATED                                                                                              9
  DEL PEAK 21(14Q32.31) WILD-TYPE                                                                                           68
D44V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 21(14Q32.31) 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)                             9
                                                                                              clus
vv                                                                                             DEL PEAK 21(14Q32.31) 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)                                         42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V30, binary
                                 cls
clus                               0  1
  DEL PEAK 21(14Q32.31) MUTATED   10  9
  DEL PEAK 21(14Q32.31) WILD-TYPE 44 50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.31) MUTATED     10    9
  DEL PEAK 21(14Q32.31) WILD-TYPE   44   50
         clus
vv        DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  ABSENT                             10                              44
  PRESENT                             9                              50
[1] 2 2
[1] FALSE
D44V31, continuous
D44V32, continuous
D44V33, binary
                                 cls
clus                               0  1
  DEL PEAK 21(14Q32.31) MUTATED    5 10
  DEL PEAK 21(14Q32.31) WILD-TYPE 30 71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.31) MUTATED      5   10
  DEL PEAK 21(14Q32.31) WILD-TYPE   30   71
                                          clus
vv                                         DEL PEAK 21(14Q32.31) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 5
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            10
                                          clus
vv                                         DEL PEAK 21(14Q32.31) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              71
[1] 2 2
[1] FALSE
D44V34, continuous
                                 vv
clus                              OTHER RADICAL HYSTERECTOMY
  DEL PEAK 21(14Q32.31) MUTATED       0                   18
  DEL PEAK 21(14Q32.31) WILD-TYPE     3                   95
                                 vv
clus                              SIMPLE HYSTERECTOMY
  DEL PEAK 21(14Q32.31) MUTATED                     3
  DEL PEAK 21(14Q32.31) WILD-TYPE                   2
D44V35, multiclass
                      clus
vv                     DEL PEAK 21(14Q32.31) MUTATED
  OTHER                                            0
  RADICAL HYSTERECTOMY                            18
  SIMPLE HYSTERECTOMY                              3
                      clus
vv                     DEL PEAK 21(14Q32.31) WILD-TYPE
  OTHER                                              3
  RADICAL HYSTERECTOMY                              95
  SIMPLE HYSTERECTOMY                                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 21(14Q32.31) MUTATED              1           7          3
  DEL PEAK 21(14Q32.31) WILD-TYPE            7          33         37
D44V36, multiclass
              clus
vv             DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  CURRENT USER                             1                               7
  FORMER USER                              7                              33
  NEVER USED                               3                              37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V37, continuous
D44V38, binary
                                 cls
clus                               0  1
  DEL PEAK 21(14Q32.31) MUTATED   12  3
  DEL PEAK 21(14Q32.31) WILD-TYPE 61 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.31) MUTATED     12    3
  DEL PEAK 21(14Q32.31) WILD-TYPE   61   11
         clus
vv        DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  ABSENT                             12                              61
  PRESENT                             3                              11
[1] 2 2
[1] FALSE
D44V39, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 21(14Q32.31) MUTATED     0    0   1    9    4  2   1    2    0   1
  DEL PEAK 21(14Q32.31) WILD-TYPE   2    1  21   42   17  1   5    4    8  12
                                 vv
clus                              T3B T4 TX
  DEL PEAK 21(14Q32.31) MUTATED     0  0  2
  DEL PEAK 21(14Q32.31) WILD-TYPE   2  1  5
D44V40, multiclass
      clus
vv     DEL PEAK 21(14Q32.31) MUTATED DEL PEAK 21(14Q32.31) WILD-TYPE
  T1A                              0                               2
  T1A1                             0                               1
  T1B                              1                              21
  T1B1                             9                              42
  T1B2                             4                              17
  T2                               2                               1
  T2A                              1                               5
  T2A1                             2                               4
  T2A2                             0                               8
  T2B                              1                              12
  T3B                              0                               2
  T4                               0                               1
  TX                               2                               5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V41, continuous

Clustering(45) Variable = DEL PEAK 22(15Q21.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(15Q21.1) MUTATED    28   7
  DEL PEAK 22(15Q21.1) WILD-TYPE 109  25
  DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE 
                            35                            134 
  DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE 
                             7                             25 
$`DEL PEAK 22(15Q21.1) MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A7CG 
       57.04        35.01        38.99        40.93        73.45       182.93 
TCGA-C5-A7CH TCGA-C5-A7UC TCGA-DR-A0ZL TCGA-DS-A7WH TCGA-EA-A439 TCGA-EA-A43B 
       25.35        17.19        87.75         7.33        14.50         1.81 
TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ 
       14.89        12.59         1.18         2.24         0.10         0.10 
TCGA-FU-A23L TCGA-FU-A40J TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
       23.84         1.35        21.67         4.11       137.16        66.81 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MU-A8JM 
       78.71        26.56        10.06         0.89         0.07         5.42 
TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       29.72         2.96         3.72         3.45         5.85 

$`DEL PEAK 22(15Q21.1) 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-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       35.61         0.46         2.43         3.58        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        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-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
        9.67        73.41        85.55        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       13.61         2.73        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS 
      118.65        22.98        16.83        16.18         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-A44S TCGA-EA-A4BA 
        1.18        14.50         1.35         1.35        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
        0.26         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.58        13.48        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO 
        0.07         4.04         0.03         0.36        23.70         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-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.47         6.12         1.22         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-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-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      147.39       117.40        96.95        81.96        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU 
       16.64        19.33        20.48        15.58         5.13         0.10 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DT 
        0.82        13.87         0.03         0.07         4.34         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE 
                        182.93                         177.04 
  DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE 
                         14.50                          13.53 
[1] "0.1 - 182.9 (14.5)" "0.0 - 177.0 (13.5)"
[1] "hr=" "1"  
D45V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 22(15Q21.1) MUTATED   20        9
  DEL PEAK 22(15Q21.1) WILD-TYPE 77       30
D45V3, multiclass
          clus
vv         DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  T1                                 20                             77
  T2+T3+T4                            9                             30
[1] 2 2
[1] FALSE
D45V4, binary
                                cls
clus                              0  1
  DEL PEAK 22(15Q21.1) MUTATED   23  5
  DEL PEAK 22(15Q21.1) WILD-TYPE 64 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q21.1) MUTATED     23    5
  DEL PEAK 22(15Q21.1) WILD-TYPE   64   35
   clus
vv  DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  0                           23                             64
  1                            5                             35
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 22(15Q21.1) MUTATED   15  1 14
  DEL PEAK 22(15Q21.1) WILD-TYPE 57  2 51
D45V5, multiclass
    clus
vv   DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  M0                           15                             57
  M1                            1                              2
  MX                           14                             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(15Q21.1) MUTATED               1                               28
  DEL PEAK 22(15Q21.1) WILD-TYPE             1                              116
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 22(15Q21.1) MUTATED                                               0
  DEL PEAK 22(15Q21.1) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 22(15Q21.1) MUTATED                                     5
  DEL PEAK 22(15Q21.1) WILD-TYPE                                  15
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 22(15Q21.1) MUTATED                                           2
  DEL PEAK 22(15Q21.1) WILD-TYPE                                         0
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 22(15Q21.1) MUTATED                                              1
  DEL PEAK 22(15Q21.1) WILD-TYPE                                            3
D45V6, multiclass
                                               clus
vv                                              DEL PEAK 22(15Q21.1) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK 22(15Q21.1) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         116
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(15Q21.1) MUTATED     4  33
  DEL PEAK 22(15Q21.1) WILD-TYPE  23 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q21.1) MUTATED      4   33
  DEL PEAK 22(15Q21.1) WILD-TYPE   23  116
     clus
vv    DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  NO                             4                             23
  YES                           33                            116
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(15Q21.1) MUTATED                                  0     4
  DEL PEAK 22(15Q21.1) WILD-TYPE                                7    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(15Q21.1) MUTATED                           6
  DEL PEAK 22(15Q21.1) WILD-TYPE                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 22(15Q21.1) MUTATED                                           1
  DEL PEAK 22(15Q21.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 22(15Q21.1) MUTATED      26
  DEL PEAK 22(15Q21.1) WILD-TYPE   104
D45V10, multiclass
                                           clus
vv                                          DEL PEAK 22(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               26
                                           clus
vv                                          DEL PEAK 22(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D45V11, binary
                                cls
clus                               0   1
  DEL PEAK 22(15Q21.1) MUTATED     2  27
  DEL PEAK 22(15Q21.1) WILD-TYPE   9 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q21.1) MUTATED      2   27
  DEL PEAK 22(15Q21.1) WILD-TYPE    9  100
                        clus
vv                       DEL PEAK 22(15Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       DEL PEAK 22(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            100
[1] 2 2
[1] FALSE
D45V12, continuous
D45V13, binary
                                cls
clus                              0  1
  DEL PEAK 22(15Q21.1) MUTATED    9  4
  DEL PEAK 22(15Q21.1) WILD-TYPE 39 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q21.1) MUTATED      9    4
  DEL PEAK 22(15Q21.1) WILD-TYPE   39   15
            clus
vv           DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  TUMOR FREE                            9                             39
  WITH TUMOR                            4                             15
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 22(15Q21.1) MUTATED         1      1       1            31       3
  DEL PEAK 22(15Q21.1) WILD-TYPE       0      9       5           116       9
D45V14, multiclass
               clus
vv              DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  NIGERIA                                  1                              0
  RUSSIA                                   1                              9
  UKRAINE                                  1                              5
  UNITED STATES                           31                            116
  VIETNAM                                  3                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 22(15Q21.1) MUTATED    2 10 23  1  1
  DEL PEAK 22(15Q21.1) WILD-TYPE 12 73 49  0  4
D45V15, multiclass
    clus
vv   DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  G1                            2                             12
  G2                           10                             73
  G3                           23                             49
  G4                            1                              0
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V16, continuous
D45V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 22(15Q21.1) MUTATED                                             2
  DEL PEAK 22(15Q21.1) WILD-TYPE                                          19
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 22(15Q21.1) MUTATED                                        2
  DEL PEAK 22(15Q21.1) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 22(15Q21.1) MUTATED                                                 0
  DEL PEAK 22(15Q21.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 22(15Q21.1) MUTATED                5                  18
  DEL PEAK 22(15Q21.1) WILD-TYPE             31                  65
D45V18, multiclass
                                                 clus
vv                                                DEL PEAK 22(15Q21.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             5
  LIFELONG NON-SMOKER                                                       18
                                                 clus
vv                                                DEL PEAK 22(15Q21.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              31
  LIFELONG NON-SMOKER                                                         65
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 22(15Q21.1) MUTATED             2       10             2        0
  DEL PEAK 22(15Q21.1) WILD-TYPE          15       27             9        5
D45V20, multiclass
               clus
vv              DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  COMBINATION                              2                             15
  EXTERNAL                                10                             27
  EXTERNAL BEAM                            2                              9
  INTERNAL                                 0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V21, binary
                                cls
clus                             0 1
  DEL PEAK 22(15Q21.1) MUTATED   3 0
  DEL PEAK 22(15Q21.1) WILD-TYPE 8 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q21.1) MUTATED      3    0
  DEL PEAK 22(15Q21.1) WILD-TYPE    8    3
     clus
vv    DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  CGY                            3                              8
  GY                             0                              3
[1] 2 2
[1] FALSE
D45V22, continuous
D45V23, continuous
D45V24, continuous
D45V25, continuous
D45V26, continuous
D45V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 22(15Q21.1) MUTATED                                     0
  DEL PEAK 22(15Q21.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 22(15Q21.1) MUTATED                                     2
  DEL PEAK 22(15Q21.1) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 22(15Q21.1) MUTATED                         1
  DEL PEAK 22(15Q21.1) WILD-TYPE                       8
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 22(15Q21.1) MUTATED                         0
  DEL PEAK 22(15Q21.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 22(15Q21.1) MUTATED                         1
  DEL PEAK 22(15Q21.1) WILD-TYPE                       4
D45V28, multiclass
                                     clus
vv                                    DEL PEAK 22(15Q21.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        1
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 22(15Q21.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                          8
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 22(15Q21.1) MUTATED                                               0
  DEL PEAK 22(15Q21.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 22(15Q21.1) MUTATED                                                2
  DEL PEAK 22(15Q21.1) WILD-TYPE                                              8
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 22(15Q21.1) MUTATED                                                                                  13
  DEL PEAK 22(15Q21.1) WILD-TYPE                                                                                41
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 22(15Q21.1) MUTATED                                                                                             15
  DEL PEAK 22(15Q21.1) WILD-TYPE                                                                                           62
D45V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 22(15Q21.1) 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)                           15
                                                                                              clus
vv                                                                                             DEL PEAK 22(15Q21.1) 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)                                        41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V30, binary
                                cls
clus                              0  1
  DEL PEAK 22(15Q21.1) MUTATED    8 11
  DEL PEAK 22(15Q21.1) WILD-TYPE 46 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q21.1) MUTATED      8   11
  DEL PEAK 22(15Q21.1) WILD-TYPE   46   48
         clus
vv        DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  ABSENT                             8                             46
  PRESENT                           11                             48
[1] 2 2
[1] FALSE
D45V31, continuous
D45V32, continuous
D45V33, binary
                                cls
clus                              0  1
  DEL PEAK 22(15Q21.1) MUTATED    9 15
  DEL PEAK 22(15Q21.1) WILD-TYPE 26 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q21.1) MUTATED      9   15
  DEL PEAK 22(15Q21.1) WILD-TYPE   26   66
                                          clus
vv                                         DEL PEAK 22(15Q21.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           15
                                          clus
vv                                         DEL PEAK 22(15Q21.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             66
[1] 2 2
[1] FALSE
D45V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 22(15Q21.1) MUTATED       1                   24                   2
  DEL PEAK 22(15Q21.1) WILD-TYPE     2                   89                   3
D45V35, multiclass
                      clus
vv                     DEL PEAK 22(15Q21.1) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           24
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     DEL PEAK 22(15Q21.1) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             89
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 22(15Q21.1) MUTATED              1           9          9
  DEL PEAK 22(15Q21.1) WILD-TYPE            7          31         31
D45V36, multiclass
              clus
vv             DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  CURRENT USER                            1                              7
  FORMER USER                             9                             31
  NEVER USED                              9                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V37, continuous
D45V38, binary
                                cls
clus                              0  1
  DEL PEAK 22(15Q21.1) MUTATED   11  3
  DEL PEAK 22(15Q21.1) WILD-TYPE 62 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q21.1) MUTATED     11    3
  DEL PEAK 22(15Q21.1) WILD-TYPE   62   11
         clus
vv        DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  ABSENT                            11                             62
  PRESENT                            3                             11
[1] 2 2
[1] FALSE
D45V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 22(15Q21.1) MUTATED     1    0   4   12    3  0   1    4    0   3
  DEL PEAK 22(15Q21.1) WILD-TYPE   1    1  18   39   18  3   5    2    8  10
                                vv
clus                             T3B T4 TX
  DEL PEAK 22(15Q21.1) MUTATED     1  0  2
  DEL PEAK 22(15Q21.1) WILD-TYPE   1  1  5
D45V40, multiclass
      clus
vv     DEL PEAK 22(15Q21.1) MUTATED DEL PEAK 22(15Q21.1) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             4                             18
  T1B1                           12                             39
  T1B2                            3                             18
  T2                              0                              3
  T2A                             1                              5
  T2A1                            4                              2
  T2A2                            0                              8
  T2B                             3                             10
  T3B                             1                              1
  T4                              0                              1
  TX                              2                              5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V41, continuous

Clustering(46) Variable = DEL PEAK 23(16Q12.1) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(16Q12.1) MUTATED    27   5
  DEL PEAK 23(16Q12.1) WILD-TYPE 110  27
  DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE 
                            32                            137 
  DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE 
                             5                             27 
$`DEL PEAK 23(16Q12.1) MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LS TCGA-C5-A2LT 
       23.67       173.29        35.01        57.73        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7CO 
       83.05        38.43        18.02       182.93       134.33        73.41 
TCGA-DR-A0ZL TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A43B 
       87.75        16.83         7.33        12.36         1.32         1.81 
TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EX-A1H6 TCGA-FU-A3TX TCGA-FU-A40J TCGA-FU-A770 
        0.53         1.18         7.92         1.48         1.35         1.12 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LK TCGA-MY-A5BF TCGA-Q1-A6DT 
      137.16        66.81        96.95        26.56         4.34         3.39 
TCGA-Q1-A73P TCGA-UC-A7PD 
        4.80        11.67 

$`DEL PEAK 23(16Q12.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        46.32        30.21        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LY 
        0.46         2.43        40.93         3.58        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
      100.14         0.82        52.01        17.85        20.42        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      101.82        15.48         9.67        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VK 
       94.95         9.34        13.61         2.73        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WI 
        2.66       117.99       118.65        22.98        16.18         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        0.76         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-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         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.96        13.58        13.48        12.59        45.96         6.64 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        0.59         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         4.47         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA 
        1.58         0.82         3.52         1.32         1.97        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC 
       21.67        20.78        14.93         4.11       147.39       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       78.71        81.96        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        0.07         2.96         3.72         3.45         5.85         3.72 
TCGA-Q1-A6DW TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        5.75         6.25        19.59         3.88        93.99 

  DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE 
                          0.53                           0.03 
  DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE 
                        182.93                         177.04 
  DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE 
                        20.845                         13.050 
[1] "0.5 - 182.9 (20.8)" "0.0 - 177.0 (13.1)"
[1] "hr=" "2.2"
D46V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 23(16Q12.1) MUTATED   23        6
  DEL PEAK 23(16Q12.1) WILD-TYPE 74       33
D46V3, multiclass
          clus
vv         DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  T1                                 23                             74
  T2+T3+T4                            6                             33
[1] 2 2
[1] FALSE
D46V4, binary
                                cls
clus                              0  1
  DEL PEAK 23(16Q12.1) MUTATED   24  5
  DEL PEAK 23(16Q12.1) WILD-TYPE 63 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q12.1) MUTATED     24    5
  DEL PEAK 23(16Q12.1) WILD-TYPE   63   35
   clus
vv  DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  0                           24                             63
  1                            5                             35
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 23(16Q12.1) MUTATED   18  0 12
  DEL PEAK 23(16Q12.1) WILD-TYPE 54  3 53
D46V5, multiclass
    clus
vv   DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  M0                           18                             54
  M1                            0                              3
  MX                           12                             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(16Q12.1) MUTATED               0                               22
  DEL PEAK 23(16Q12.1) WILD-TYPE             2                              122
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 23(16Q12.1) MUTATED                                               3
  DEL PEAK 23(16Q12.1) WILD-TYPE                                             1
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 23(16Q12.1) MUTATED                                     9
  DEL PEAK 23(16Q12.1) WILD-TYPE                                  11
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 23(16Q12.1) MUTATED                                           1
  DEL PEAK 23(16Q12.1) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 23(16Q12.1) MUTATED                                              0
  DEL PEAK 23(16Q12.1) WILD-TYPE                                            4
D46V6, multiclass
                                               clus
vv                                              DEL PEAK 23(16Q12.1) 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                                              DEL PEAK 23(16Q12.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         122
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       11
  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"
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(16Q12.1) MUTATED     4  31
  DEL PEAK 23(16Q12.1) WILD-TYPE  23 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q12.1) MUTATED      4   31
  DEL PEAK 23(16Q12.1) WILD-TYPE   23  118
     clus
vv    DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  NO                             4                             23
  YES                           31                            118
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(16Q12.1) MUTATED                                  1     2
  DEL PEAK 23(16Q12.1) WILD-TYPE                                6    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(16Q12.1) MUTATED                           1
  DEL PEAK 23(16Q12.1) WILD-TYPE                        17
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 23(16Q12.1) MUTATED                                           0
  DEL PEAK 23(16Q12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 23(16Q12.1) MUTATED      30
  DEL PEAK 23(16Q12.1) WILD-TYPE   100
D46V10, multiclass
                                           clus
vv                                          DEL PEAK 23(16Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               30
                                           clus
vv                                          DEL PEAK 23(16Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D46V11, binary
                                cls
clus                               0   1
  DEL PEAK 23(16Q12.1) MUTATED     1  25
  DEL PEAK 23(16Q12.1) WILD-TYPE  10 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q12.1) MUTATED      1   25
  DEL PEAK 23(16Q12.1) WILD-TYPE   10  102
                        clus
vv                       DEL PEAK 23(16Q12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 23(16Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            102
[1] 2 2
[1] FALSE
D46V12, continuous
D46V13, binary
                                cls
clus                              0  1
  DEL PEAK 23(16Q12.1) MUTATED   10  2
  DEL PEAK 23(16Q12.1) WILD-TYPE 38 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q12.1) MUTATED     10    2
  DEL PEAK 23(16Q12.1) WILD-TYPE   38   17
            clus
vv           DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  TUMOR FREE                           10                             38
  WITH TUMOR                            2                             17
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 23(16Q12.1) MUTATED         0      2       1            31       1
  DEL PEAK 23(16Q12.1) WILD-TYPE       1      8       5           116      11
D46V14, multiclass
               clus
vv              DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  1                              5
  UNITED STATES                           31                            116
  VIETNAM                                  1                             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 23(16Q12.1) MUTATED    5 17 12  0  1
  DEL PEAK 23(16Q12.1) WILD-TYPE  9 66 60  1  4
D46V15, multiclass
    clus
vv   DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  G1                            5                              9
  G2                           17                             66
  G3                           12                             60
  G4                            0                              1
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V16, continuous
D46V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 23(16Q12.1) MUTATED                                             3
  DEL PEAK 23(16Q12.1) WILD-TYPE                                          18
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 23(16Q12.1) MUTATED                                        2
  DEL PEAK 23(16Q12.1) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 23(16Q12.1) MUTATED                                                 1
  DEL PEAK 23(16Q12.1) WILD-TYPE                                               0
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 23(16Q12.1) MUTATED                6                  19
  DEL PEAK 23(16Q12.1) WILD-TYPE             30                  64
D46V18, multiclass
                                                 clus
vv                                                DEL PEAK 23(16Q12.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                             6
  LIFELONG NON-SMOKER                                                       19
                                                 clus
vv                                                DEL PEAK 23(16Q12.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              0
  CURRENT SMOKER                                                              30
  LIFELONG NON-SMOKER                                                         64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 23(16Q12.1) MUTATED             2        8             2        2
  DEL PEAK 23(16Q12.1) WILD-TYPE          15       29             9        3
D46V20, multiclass
               clus
vv              DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  COMBINATION                              2                             15
  EXTERNAL                                 8                             29
  EXTERNAL BEAM                            2                              9
  INTERNAL                                 2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V21, binary
                                cls
clus                             0 1
  DEL PEAK 23(16Q12.1) MUTATED   2 0
  DEL PEAK 23(16Q12.1) WILD-TYPE 9 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q12.1) MUTATED      2    0
  DEL PEAK 23(16Q12.1) WILD-TYPE    9    3
     clus
vv    DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  CGY                            2                              9
  GY                             0                              3
[1] 2 2
[1] FALSE
D46V22, continuous
D46V23, continuous
D46V24, continuous
D46V25, continuous
D46V26, continuous
D46V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 23(16Q12.1) MUTATED                                     0
  DEL PEAK 23(16Q12.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 23(16Q12.1) MUTATED                                     2
  DEL PEAK 23(16Q12.1) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 23(16Q12.1) MUTATED                         1
  DEL PEAK 23(16Q12.1) WILD-TYPE                       8
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 23(16Q12.1) MUTATED                         0
  DEL PEAK 23(16Q12.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 23(16Q12.1) MUTATED                         1
  DEL PEAK 23(16Q12.1) WILD-TYPE                       4
D46V28, multiclass
                                     clus
vv                                    DEL PEAK 23(16Q12.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        1
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 23(16Q12.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                          8
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 23(16Q12.1) MUTATED                                               0
  DEL PEAK 23(16Q12.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 23(16Q12.1) MUTATED                                                0
  DEL PEAK 23(16Q12.1) WILD-TYPE                                             10
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 23(16Q12.1) MUTATED                                                                                  15
  DEL PEAK 23(16Q12.1) WILD-TYPE                                                                                39
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 23(16Q12.1) MUTATED                                                                                             12
  DEL PEAK 23(16Q12.1) WILD-TYPE                                                                                           65
D46V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 23(16Q12.1) 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)                                      15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           12
                                                                                              clus
vv                                                                                             DEL PEAK 23(16Q12.1) 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)                                        39
  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"
D46V30, binary
                                cls
clus                              0  1
  DEL PEAK 23(16Q12.1) MUTATED   12 11
  DEL PEAK 23(16Q12.1) WILD-TYPE 42 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q12.1) MUTATED     12   11
  DEL PEAK 23(16Q12.1) WILD-TYPE   42   48
         clus
vv        DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  ABSENT                            12                             42
  PRESENT                           11                             48
[1] 2 2
[1] FALSE
D46V31, continuous
D46V32, continuous
D46V33, binary
                                cls
clus                              0  1
  DEL PEAK 23(16Q12.1) MUTATED    8 10
  DEL PEAK 23(16Q12.1) WILD-TYPE 27 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q12.1) MUTATED      8   10
  DEL PEAK 23(16Q12.1) WILD-TYPE   27   71
                                          clus
vv                                         DEL PEAK 23(16Q12.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                8
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           10
                                          clus
vv                                         DEL PEAK 23(16Q12.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             71
[1] 2 2
[1] FALSE
D46V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 23(16Q12.1) MUTATED       2                   23                   2
  DEL PEAK 23(16Q12.1) WILD-TYPE     1                   90                   3
D46V35, multiclass
                      clus
vv                     DEL PEAK 23(16Q12.1) MUTATED
  OTHER                                           2
  RADICAL HYSTERECTOMY                           23
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     DEL PEAK 23(16Q12.1) WILD-TYPE
  OTHER                                             1
  RADICAL HYSTERECTOMY                             90
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 23(16Q12.1) MUTATED              2           8         10
  DEL PEAK 23(16Q12.1) WILD-TYPE            6          32         30
D46V36, multiclass
              clus
vv             DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                             8                             32
  NEVER USED                             10                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V37, continuous
D46V38, binary
                                cls
clus                              0  1
  DEL PEAK 23(16Q12.1) MUTATED   19  1
  DEL PEAK 23(16Q12.1) WILD-TYPE 54 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q12.1) MUTATED     19    1
  DEL PEAK 23(16Q12.1) WILD-TYPE   54   13
         clus
vv        DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  ABSENT                            19                             54
  PRESENT                            1                             13
[1] 2 2
[1] FALSE
D46V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 23(16Q12.1) MUTATED     0    0   7   11    5  1   1    1    2   0
  DEL PEAK 23(16Q12.1) WILD-TYPE   2    1  15   40   16  2   5    5    6  13
                                vv
clus                             T3B T4 TX
  DEL PEAK 23(16Q12.1) MUTATED     1  0  1
  DEL PEAK 23(16Q12.1) WILD-TYPE   1  1  6
D46V40, multiclass
      clus
vv     DEL PEAK 23(16Q12.1) MUTATED DEL PEAK 23(16Q12.1) WILD-TYPE
  T1A                             0                              2
  T1A1                            0                              1
  T1B                             7                             15
  T1B1                           11                             40
  T1B2                            5                             16
  T2                              1                              2
  T2A                             1                              5
  T2A1                            1                              5
  T2A2                            2                              6
  T2B                             0                             13
  T3B                             1                              1
  T4                              0                              1
  TX                              1                              6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V41, continuous

Clustering(47) Variable = DEL PEAK 24(16Q23.1) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(16Q23.1) MUTATED    27   3
  DEL PEAK 24(16Q23.1) WILD-TYPE 110  29
  DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE 
                            30                            139 
  DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE 
                             3                             29 
$`DEL PEAK 24(16Q23.1) MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LS TCGA-C5-A2LT 
       23.67       173.29        35.01        57.73        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CO 
       83.05        38.43        52.01        18.02       182.93        73.41 
TCGA-C5-A7UH TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2RJ 
       60.69        22.98         7.33         1.81        14.89         1.18 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A69M TCGA-FU-A3EO TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.03         7.92         6.12         2.17         1.58         1.48 
TCGA-FU-A40J TCGA-FU-A770 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-MY-A5BF 
        1.35         1.12       137.16        66.81        96.95         4.34 

$`DEL PEAK 24(16Q23.1) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        46.32        30.21        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LY 
        0.46         2.43        40.93         3.58        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
      100.14         0.82        17.85        20.42        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
      134.33        15.48         9.67        17.19        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        9.34        13.61         2.73        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-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-A411 TCGA-EA-A439 
       13.05         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.66        12.82         0.26         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        6.64         0.53         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-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-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A23K 
        0.10        20.35         6.94        14.70         4.47         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3WB 
       23.84         0.92         0.66         1.02         1.45         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        3.52         1.32         1.97        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
       14.93         4.11       147.39       117.40        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        14.43        16.64        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96         3.72         3.45         5.85         3.39         3.72 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.75         4.80         6.25        19.59         3.88        11.67 
TCGA-UC-A7PF 
       93.99 

  DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE 
                        182.93                         177.04 
  DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE 
                        23.325                         12.820 
[1] "0.0 - 182.9 (23.3)" "0.0 - 177.0 (12.8)"
[1] "hr=" "3.3"
D47V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 24(16Q23.1) MUTATED   19        8
  DEL PEAK 24(16Q23.1) WILD-TYPE 78       31
D47V3, multiclass
          clus
vv         DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  T1                                 19                             78
  T2+T3+T4                            8                             31
[1] 2 2
[1] FALSE
D47V4, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q23.1) MUTATED   20  7
  DEL PEAK 24(16Q23.1) WILD-TYPE 67 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.1) MUTATED     20    7
  DEL PEAK 24(16Q23.1) WILD-TYPE   67   33
   clus
vv  DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  0                           20                             67
  1                            7                             33
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 24(16Q23.1) MUTATED   16  0 11
  DEL PEAK 24(16Q23.1) WILD-TYPE 56  3 54
D47V5, multiclass
    clus
vv   DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  M0                           16                             56
  M1                            0                              3
  MX                           11                             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(16Q23.1) MUTATED               0                               20
  DEL PEAK 24(16Q23.1) WILD-TYPE             2                              124
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 24(16Q23.1) MUTATED                                               3
  DEL PEAK 24(16Q23.1) WILD-TYPE                                             1
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 24(16Q23.1) MUTATED                                     9
  DEL PEAK 24(16Q23.1) WILD-TYPE                                  11
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 24(16Q23.1) MUTATED                                           2
  DEL PEAK 24(16Q23.1) WILD-TYPE                                         0
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 24(16Q23.1) MUTATED                                              0
  DEL PEAK 24(16Q23.1) WILD-TYPE                                            4
D47V6, multiclass
                                               clus
vv                                              DEL PEAK 24(16Q23.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        20
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              DEL PEAK 24(16Q23.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         124
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  0
  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"
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.1) MUTATED     5  29
  DEL PEAK 24(16Q23.1) WILD-TYPE  22 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.1) MUTATED      5   29
  DEL PEAK 24(16Q23.1) WILD-TYPE   22  120
     clus
vv    DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  NO                             5                             22
  YES                           29                            120
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(16Q23.1) MUTATED                                  0     1
  DEL PEAK 24(16Q23.1) WILD-TYPE                                7    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(16Q23.1) MUTATED                           0
  DEL PEAK 24(16Q23.1) WILD-TYPE                        18
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 24(16Q23.1) MUTATED                                           0
  DEL PEAK 24(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 24(16Q23.1) MUTATED      31
  DEL PEAK 24(16Q23.1) WILD-TYPE    99
D47V10, multiclass
                                           clus
vv                                          DEL PEAK 24(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               31
                                           clus
vv                                          DEL PEAK 24(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       7
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 99
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.1) MUTATED     1  25
  DEL PEAK 24(16Q23.1) WILD-TYPE  10 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.1) MUTATED      1   25
  DEL PEAK 24(16Q23.1) WILD-TYPE   10  102
                        clus
vv                       DEL PEAK 24(16Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 24(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            102
[1] 2 2
[1] FALSE
D47V12, continuous
D47V13, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q23.1) MUTATED   10  1
  DEL PEAK 24(16Q23.1) WILD-TYPE 38 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.1) MUTATED     10    1
  DEL PEAK 24(16Q23.1) WILD-TYPE   38   18
            clus
vv           DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  TUMOR FREE                           10                             38
  WITH TUMOR                            1                             18
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 24(16Q23.1) MUTATED         0      1       1            31       1
  DEL PEAK 24(16Q23.1) WILD-TYPE       1      9       5           116      11
D47V14, multiclass
               clus
vv              DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   1                              9
  UKRAINE                                  1                              5
  UNITED STATES                           31                            116
  VIETNAM                                  1                             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 24(16Q23.1) MUTATED    4 15 15  0  0
  DEL PEAK 24(16Q23.1) WILD-TYPE 10 68 57  1  5
D47V15, multiclass
    clus
vv   DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  G1                            4                             10
  G2                           15                             68
  G3                           15                             57
  G4                            0                              1
  GX                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V16, continuous
D47V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 24(16Q23.1) MUTATED                                             5
  DEL PEAK 24(16Q23.1) WILD-TYPE                                          16
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 24(16Q23.1) MUTATED                                        3
  DEL PEAK 24(16Q23.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 24(16Q23.1) MUTATED                                                 0
  DEL PEAK 24(16Q23.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 24(16Q23.1) MUTATED                7                  14
  DEL PEAK 24(16Q23.1) WILD-TYPE             29                  69
D47V18, multiclass
                                                 clus
vv                                                DEL PEAK 24(16Q23.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             7
  LIFELONG NON-SMOKER                                                       14
                                                 clus
vv                                                DEL PEAK 24(16Q23.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              29
  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"
D47V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 24(16Q23.1) MUTATED             2        5             3        2
  DEL PEAK 24(16Q23.1) WILD-TYPE          15       32             8        3
D47V20, multiclass
               clus
vv              DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  COMBINATION                              2                             15
  EXTERNAL                                 5                             32
  EXTERNAL BEAM                            3                              8
  INTERNAL                                 2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V21, binary
                                cls
clus                             0 1
  DEL PEAK 24(16Q23.1) MUTATED   2 0
  DEL PEAK 24(16Q23.1) WILD-TYPE 9 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.1) MUTATED      2    0
  DEL PEAK 24(16Q23.1) WILD-TYPE    9    3
     clus
vv    DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  CGY                            2                              9
  GY                             0                              3
[1] 2 2
[1] FALSE
D47V22, continuous
D47V23, continuous
D47V24, continuous
D47V25, continuous
D47V26, continuous
D47V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 24(16Q23.1) MUTATED                                     0
  DEL PEAK 24(16Q23.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 24(16Q23.1) MUTATED                                     1
  DEL PEAK 24(16Q23.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 24(16Q23.1) MUTATED                         1
  DEL PEAK 24(16Q23.1) WILD-TYPE                       8
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 24(16Q23.1) MUTATED                         0
  DEL PEAK 24(16Q23.1) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 24(16Q23.1) MUTATED                         2
  DEL PEAK 24(16Q23.1) WILD-TYPE                       3
D47V28, multiclass
                                     clus
vv                                    DEL PEAK 24(16Q23.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        1
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 24(16Q23.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          8
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 24(16Q23.1) MUTATED                                               0
  DEL PEAK 24(16Q23.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 24(16Q23.1) MUTATED                                                0
  DEL PEAK 24(16Q23.1) WILD-TYPE                                             10
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 24(16Q23.1) MUTATED                                                                                  12
  DEL PEAK 24(16Q23.1) WILD-TYPE                                                                                42
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 24(16Q23.1) MUTATED                                                                                             12
  DEL PEAK 24(16Q23.1) WILD-TYPE                                                                                           65
D47V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 24(16Q23.1) 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)                                      12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           12
                                                                                              clus
vv                                                                                             DEL PEAK 24(16Q23.1) 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)                                        42
  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"
D47V30, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q23.1) MUTATED   10 11
  DEL PEAK 24(16Q23.1) WILD-TYPE 44 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.1) MUTATED     10   11
  DEL PEAK 24(16Q23.1) WILD-TYPE   44   48
         clus
vv        DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  ABSENT                            10                             44
  PRESENT                           11                             48
[1] 2 2
[1] FALSE
D47V31, continuous
D47V32, continuous
D47V33, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q23.1) MUTATED    6  9
  DEL PEAK 24(16Q23.1) WILD-TYPE 29 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.1) MUTATED      6    9
  DEL PEAK 24(16Q23.1) WILD-TYPE   29   72
                                          clus
vv                                         DEL PEAK 24(16Q23.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            9
                                          clus
vv                                         DEL PEAK 24(16Q23.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             72
[1] 2 2
[1] FALSE
D47V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 24(16Q23.1) MUTATED       2                   20                   2
  DEL PEAK 24(16Q23.1) WILD-TYPE     1                   93                   3
D47V35, multiclass
                      clus
vv                     DEL PEAK 24(16Q23.1) MUTATED
  OTHER                                           2
  RADICAL HYSTERECTOMY                           20
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     DEL PEAK 24(16Q23.1) WILD-TYPE
  OTHER                                             1
  RADICAL HYSTERECTOMY                             93
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 24(16Q23.1) MUTATED              2          10          8
  DEL PEAK 24(16Q23.1) WILD-TYPE            6          30         32
D47V36, multiclass
              clus
vv             DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                            10                             30
  NEVER USED                              8                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V37, continuous
D47V38, binary
                                cls
clus                              0  1
  DEL PEAK 24(16Q23.1) MUTATED   16  2
  DEL PEAK 24(16Q23.1) WILD-TYPE 57 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.1) MUTATED     16    2
  DEL PEAK 24(16Q23.1) WILD-TYPE   57   12
         clus
vv        DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  ABSENT                            16                             57
  PRESENT                            2                             12
[1] 2 2
[1] FALSE
D47V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 24(16Q23.1) MUTATED     0    0   4   10    5  1   0    1    2   2
  DEL PEAK 24(16Q23.1) WILD-TYPE   2    1  18   41   16  2   6    5    6  11
                                vv
clus                             T3B T4 TX
  DEL PEAK 24(16Q23.1) MUTATED     2  0  1
  DEL PEAK 24(16Q23.1) WILD-TYPE   0  1  6
D47V40, multiclass
      clus
vv     DEL PEAK 24(16Q23.1) MUTATED DEL PEAK 24(16Q23.1) WILD-TYPE
  T1A                             0                              2
  T1A1                            0                              1
  T1B                             4                             18
  T1B1                           10                             41
  T1B2                            5                             16
  T2                              1                              2
  T2A                             0                              6
  T2A1                            1                              5
  T2A2                            2                              6
  T2B                             2                             11
  T3B                             2                              0
  T4                              0                              1
  TX                              1                              6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V41, continuous

Clustering(48) Variable = DEL PEAK 25(17P12) MUTATION ANALYSIS
D48V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 25(17P12) MUTATED   41 14
  DEL PEAK 25(17P12) WILD-TYPE 96 18
  DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE 
                          55                          114 
  DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE 
                          14                           18 
$`DEL PEAK 25(17P12) MUTATED`
TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN 
       23.67        68.84        18.74       144.16       173.29         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX 
       19.86        67.46        38.99        40.93        73.18        83.05 
TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X3 
       38.43        52.01        15.48        73.41        17.19         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ 
       13.61         2.73        87.75         2.66       118.65        22.98 
TCGA-EA-A1QT TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       12.36        14.50        12.66        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM 
       13.48        45.96         0.53         0.03         1.18         2.24 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A3EO 
        0.10         0.10        20.35         6.94         6.12         2.17 
TCGA-FU-A3NI TCGA-IR-A3LB TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A69B 
        1.45        66.81        78.71        26.56        16.64        10.06 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        0.10         0.89         0.03         2.96         3.45         3.39 
TCGA-RA-A741 
        3.88 

$`DEL PEAK 25(17P12) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM 
       49.48        57.04        11.44        36.56       177.04        82.85 
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-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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14         0.82        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7UE 
      182.93        25.35       101.82       134.33         9.67        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A5RQ 
       60.69        94.95        58.88        36.76       117.99        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18         7.33         8.28         0.76         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-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-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB 
       13.91         0.69        12.59         6.64         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK 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-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        7.92        14.70         4.47         1.22        23.84         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-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC 
       20.78        14.93         4.11       147.39       137.16       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK 
       96.95        81.96        36.36        14.43        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM 
       15.58         5.13         0.07         0.82        13.87         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
       29.72         0.07         4.34         3.72         5.85         3.72 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF 
        5.75         4.80         6.25        19.59        11.67        93.99 

  DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE 
                        0.03                         0.03 
  DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE 
                      173.29                       182.93 
  DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE 
                      14.500                       12.705 
[1] "0.0 - 173.3 (14.5)" "0.0 - 182.9 (12.7)"
[1] "hr=" "1.5"
D48V2, continuous
                              vv
clus                           T1 T2+T3+T4
  DEL PEAK 25(17P12) MUTATED   26       13
  DEL PEAK 25(17P12) WILD-TYPE 71       26
D48V3, multiclass
          clus
vv         DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  T1                               26                           71
  T2+T3+T4                         13                           26
[1] 2 2
[1] FALSE
D48V4, binary
                              cls
clus                            0  1
  DEL PEAK 25(17P12) MUTATED   24 11
  DEL PEAK 25(17P12) WILD-TYPE 63 29
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(17P12) MUTATED     24   11
  DEL PEAK 25(17P12) WILD-TYPE   63   29
   clus
vv  DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  0                         24                           63
  1                         11                           29
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  DEL PEAK 25(17P12) MUTATED   25  0 16
  DEL PEAK 25(17P12) WILD-TYPE 47  3 49
D48V5, multiclass
    clus
vv   DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  M0                         25                           47
  M1                          0                            3
  MX                         16                           49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(17P12) MUTATED               0                               52
  DEL PEAK 25(17P12) WILD-TYPE             2                               92
                              vv
clus                           ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 25(17P12) MUTATED                                               0
  DEL PEAK 25(17P12) WILD-TYPE                                             4
                              vv
clus                           ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 25(17P12) MUTATED                                     5
  DEL PEAK 25(17P12) WILD-TYPE                                  15
                              vv
clus                           ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 25(17P12) MUTATED                                           0
  DEL PEAK 25(17P12) WILD-TYPE                                         2
                              vv
clus                           MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 25(17P12) MUTATED                                              1
  DEL PEAK 25(17P12) WILD-TYPE                                            3
D48V6, multiclass
                                               clus
vv                                              DEL PEAK 25(17P12) MUTATED
  ADENOSQUAMOUS                                                          0
  CERVICAL SQUAMOUS CELL CARCINOMA                                      52
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                          0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                    5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                              0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                           1
                                               clus
vv                                              DEL PEAK 25(17P12) WILD-TYPE
  ADENOSQUAMOUS                                                            2
  CERVICAL SQUAMOUS CELL CARCINOMA                                        92
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     15
  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"
D48V7, binary
                              cls
clus                             0   1
  DEL PEAK 25(17P12) MUTATED    12  46
  DEL PEAK 25(17P12) WILD-TYPE  15 103
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(17P12) MUTATED     12   46
  DEL PEAK 25(17P12) WILD-TYPE   15  103
     clus
vv    DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  NO                          12                           15
  YES                         46                          103
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(17P12) MUTATED                                  2     8
  DEL PEAK 25(17P12) WILD-TYPE                                5     7
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(17P12) MUTATED                           6
  DEL PEAK 25(17P12) WILD-TYPE                        12
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 25(17P12) MUTATED                                           1    40
  DEL PEAK 25(17P12) WILD-TYPE                                         0    90
D48V10, multiclass
                                           clus
vv                                          DEL PEAK 25(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              8
  BLACK OR AFRICAN AMERICAN                                          6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             40
                                           clus
vv                                          DEL PEAK 25(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     5
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               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"
D48V11, binary
                              cls
clus                            0  1
  DEL PEAK 25(17P12) MUTATED    3 40
  DEL PEAK 25(17P12) WILD-TYPE  8 87
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(17P12) MUTATED      3   40
  DEL PEAK 25(17P12) WILD-TYPE    8   87
                        clus
vv                       DEL PEAK 25(17P12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         40
                        clus
vv                       DEL PEAK 25(17P12) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           87
[1] 2 2
[1] FALSE
D48V12, continuous
D48V13, binary
                              cls
clus                            0  1
  DEL PEAK 25(17P12) MUTATED   19  7
  DEL PEAK 25(17P12) WILD-TYPE 29 12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(17P12) MUTATED     19    7
  DEL PEAK 25(17P12) WILD-TYPE   29   12
            clus
vv           DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  TUMOR FREE                         19                           29
  WITH TUMOR                          7                           12
[1] 2 2
[1] FALSE
                              vv
clus                           NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 25(17P12) MUTATED         1      1       1            48       7
  DEL PEAK 25(17P12) WILD-TYPE       0      9       5            99       5
D48V14, multiclass
               clus
vv              DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  NIGERIA                                1                            0
  RUSSIA                                 1                            9
  UKRAINE                                1                            5
  UNITED STATES                         48                           99
  VIETNAM                                7                            5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           G1 G2 G3 G4 GX
  DEL PEAK 25(17P12) MUTATED    2 25 27  1  3
  DEL PEAK 25(17P12) WILD-TYPE 12 58 45  0  2
D48V15, multiclass
    clus
vv   DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  G1                          2                           12
  G2                         25                           58
  G3                         27                           45
  G4                          1                            0
  GX                          3                            2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V16, continuous
D48V17, continuous
                              vv
clus                           CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 25(17P12) MUTATED                                             7
  DEL PEAK 25(17P12) WILD-TYPE                                          14
                              vv
clus                           CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 25(17P12) MUTATED                                        6
  DEL PEAK 25(17P12) WILD-TYPE                                      2
                              vv
clus                           CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 25(17P12) MUTATED                                                 0
  DEL PEAK 25(17P12) WILD-TYPE                                               1
                              vv
clus                           CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 25(17P12) MUTATED               11                  21
  DEL PEAK 25(17P12) WILD-TYPE             25                  62
D48V18, multiclass
                                                 clus
vv                                                DEL PEAK 25(17P12) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                              7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                   6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                          0
  CURRENT SMOKER                                                          11
  LIFELONG NON-SMOKER                                                     21
                                                 clus
vv                                                DEL PEAK 25(17P12) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            1
  CURRENT SMOKER                                                            25
  LIFELONG NON-SMOKER                                                       62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V19, continuous
                              vv
clus                           COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 25(17P12) MUTATED             9       12             3        3
  DEL PEAK 25(17P12) WILD-TYPE           8       25             8        2
D48V20, multiclass
               clus
vv              DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  COMBINATION                            9                            8
  EXTERNAL                              12                           25
  EXTERNAL BEAM                          3                            8
  INTERNAL                               3                            2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V21, binary
                              cls
clus                           0 1
  DEL PEAK 25(17P12) MUTATED   3 2
  DEL PEAK 25(17P12) WILD-TYPE 8 1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(17P12) MUTATED      3    2
  DEL PEAK 25(17P12) WILD-TYPE    8    1
     clus
vv    DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  CGY                          3                            8
  GY                           2                            1
[1] 2 2
[1] FALSE
D48V22, continuous
D48V23, continuous
D48V24, continuous
D48V25, continuous
D48V26, continuous
D48V27, continuous
                              vv
clus                           MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 25(17P12) MUTATED                                     0
  DEL PEAK 25(17P12) WILD-TYPE                                   2
                              vv
clus                           MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 25(17P12) MUTATED                                     3
  DEL PEAK 25(17P12) WILD-TYPE                                   3
                              vv
clus                           OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 25(17P12) MUTATED                         5                       0
  DEL PEAK 25(17P12) WILD-TYPE                       4                       1
                              vv
clus                           POSITIVE VAGINAL MARGIN
  DEL PEAK 25(17P12) MUTATED                         3
  DEL PEAK 25(17P12) WILD-TYPE                       2
D48V28, multiclass
                                     clus
vv                                    DEL PEAK 25(17P12) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                          0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                          3
  OTHER LOCATION, SPECIFY                                      5
  POSITIVE BLADDER MARGIN                                      0
  POSITIVE VAGINAL MARGIN                                      3
                                     clus
vv                                    DEL PEAK 25(17P12) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            3
  OTHER LOCATION, SPECIFY                                        4
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        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)
  DEL PEAK 25(17P12) MUTATED                                               1
  DEL PEAK 25(17P12) WILD-TYPE                                             1
                              vv
clus                           PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 25(17P12) MUTATED                                                5
  DEL PEAK 25(17P12) WILD-TYPE                                              5
                              vv
clus                           POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 25(17P12) MUTATED                                                                                  21
  DEL PEAK 25(17P12) WILD-TYPE                                                                                33
                              vv
clus                           PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 25(17P12) MUTATED                                                                                             20
  DEL PEAK 25(17P12) WILD-TYPE                                                                                           57
D48V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 25(17P12) 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)                                    21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                         20
                                                                                              clus
vv                                                                                             DEL PEAK 25(17P12) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                          5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                      33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V30, binary
                              cls
clus                            0  1
  DEL PEAK 25(17P12) MUTATED   15 19
  DEL PEAK 25(17P12) WILD-TYPE 39 40
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(17P12) MUTATED     15   19
  DEL PEAK 25(17P12) WILD-TYPE   39   40
         clus
vv        DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  ABSENT                          15                           39
  PRESENT                         19                           40
[1] 2 2
[1] FALSE
D48V31, continuous
D48V32, continuous
D48V33, binary
                              cls
clus                            0  1
  DEL PEAK 25(17P12) MUTATED   15 29
  DEL PEAK 25(17P12) WILD-TYPE 20 52
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(17P12) MUTATED     15   29
  DEL PEAK 25(17P12) WILD-TYPE   20   52
                                          clus
vv                                         DEL PEAK 25(17P12) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                             15
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                         29
                                          clus
vv                                         DEL PEAK 25(17P12) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                               20
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           52
[1] 2 2
[1] FALSE
D48V34, continuous
                              vv
clus                           OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 25(17P12) MUTATED       1                   32                   1
  DEL PEAK 25(17P12) WILD-TYPE     2                   81                   4
D48V35, multiclass
                      clus
vv                     DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  OTHER                                         1                            2
  RADICAL HYSTERECTOMY                         32                           81
  SIMPLE HYSTERECTOMY                           1                            4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CURRENT USER FORMER USER NEVER USED
  DEL PEAK 25(17P12) MUTATED              2          13         12
  DEL PEAK 25(17P12) WILD-TYPE            6          27         28
D48V36, multiclass
              clus
vv             DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  CURRENT USER                          2                            6
  FORMER USER                          13                           27
  NEVER USED                           12                           28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V37, continuous
D48V38, binary
                              cls
clus                            0  1
  DEL PEAK 25(17P12) MUTATED   22  3
  DEL PEAK 25(17P12) WILD-TYPE 51 11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(17P12) MUTATED     22    3
  DEL PEAK 25(17P12) WILD-TYPE   51   11
         clus
vv        DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  ABSENT                          22                           51
  PRESENT                          3                           11
[1] 2 2
[1] FALSE
D48V39, continuous
                              vv
clus                           T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 25(17P12) MUTATED     1    1   6   13    5  2   1    3    1   5   1
  DEL PEAK 25(17P12) WILD-TYPE   1    0  16   38   16  1   5    3    7   8   1
                              vv
clus                           T4 TX
  DEL PEAK 25(17P12) MUTATED    0  3
  DEL PEAK 25(17P12) WILD-TYPE  1  4
D48V40, multiclass
      clus
vv     DEL PEAK 25(17P12) MUTATED DEL PEAK 25(17P12) WILD-TYPE
  T1A                           1                            1
  T1A1                          1                            0
  T1B                           6                           16
  T1B1                         13                           38
  T1B2                          5                           16
  T2                            2                            1
  T2A                           1                            5
  T2A1                          3                            3
  T2A2                          1                            7
  T2B                           5                            8
  T3B                           1                            1
  T4                            0                            1
  TX                            3                            4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V41, continuous

Clustering(49) Variable = DEL PEAK 26(17Q25.3) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(17Q25.3) MUTATED    22   7
  DEL PEAK 26(17Q25.3) WILD-TYPE 115  25
  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE 
                            29                            140 
  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE 
                             7                             25 
$`DEL PEAK 26(17Q25.3) MUTATED`
TCGA-C5-A1BN TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A7UC TCGA-C5-A7UH 
        5.46        38.99        40.93        73.18        17.19        60.69 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR 
       13.61         2.73        36.76       118.65        12.36         1.32 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RN 
        6.64         0.53         0.59         0.03         1.18         0.10 
TCGA-EK-A3GJ TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-HM-A4S6 TCGA-IR-A3LK 
        0.10         0.66         1.45         1.58        14.93        26.56 
TCGA-JW-A5VI TCGA-JW-A5VL TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
       16.64        15.58         0.07         0.82        13.87 

$`DEL PEAK 26(17Q25.3) 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-A1BQ 
       36.56       144.16       177.04       173.29        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-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-A1MP TCGA-C5-A2LS 
       53.16        35.61         0.46         2.43         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        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE 
      101.82       134.33        15.48         9.67        73.41        85.55 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       94.95         9.34        87.75        58.88         2.66       117.99 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A3HQ TCGA-EA-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-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
        1.35         1.35        14.50         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.26        14.89         1.48        13.91         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2RB 
       14.96        13.58        13.48        12.59        45.96         0.07 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GK 
        4.04         0.36        23.70         2.24         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
        6.12         1.22        23.84         0.92         2.17         1.02 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.12        25.41        21.67        20.78         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-A852 
       36.36        14.43        19.33        20.48        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.10         0.89         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE 
                        118.65                         182.93 
  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE 
                          6.64                          14.17 
[1] "0.0 - 118.7 (6.6)"  "0.0 - 182.9 (14.2)"
[1] "hr=" "2.1"
D49V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 26(17Q25.3) MUTATED   19        6
  DEL PEAK 26(17Q25.3) WILD-TYPE 78       33
D49V3, multiclass
          clus
vv         DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  T1                                 19                             78
  T2+T3+T4                            6                             33
[1] 2 2
[1] FALSE
D49V4, binary
                                cls
clus                              0  1
  DEL PEAK 26(17Q25.3) MUTATED   15  8
  DEL PEAK 26(17Q25.3) WILD-TYPE 72 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17Q25.3) MUTATED     15    8
  DEL PEAK 26(17Q25.3) WILD-TYPE   72   32
   clus
vv  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  0                           15                             72
  1                            8                             32
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 26(17Q25.3) MUTATED   12  0 12
  DEL PEAK 26(17Q25.3) WILD-TYPE 60  3 53
D49V5, multiclass
    clus
vv   DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  M0                           12                             60
  M1                            0                              3
  MX                           12                             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(17Q25.3) MUTATED               0                               30
  DEL PEAK 26(17Q25.3) WILD-TYPE             2                              114
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 26(17Q25.3) MUTATED                                               0
  DEL PEAK 26(17Q25.3) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 26(17Q25.3) MUTATED                                     0
  DEL PEAK 26(17Q25.3) WILD-TYPE                                  20
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 26(17Q25.3) MUTATED                                           0
  DEL PEAK 26(17Q25.3) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 26(17Q25.3) MUTATED                                              1
  DEL PEAK 26(17Q25.3) WILD-TYPE                                            3
D49V6, multiclass
                                               clus
vv                                              DEL PEAK 26(17Q25.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        30
  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                                              DEL PEAK 26(17Q25.3) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         114
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(17Q25.3) MUTATED     5  26
  DEL PEAK 26(17Q25.3) WILD-TYPE  22 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17Q25.3) MUTATED      5   26
  DEL PEAK 26(17Q25.3) WILD-TYPE   22  123
     clus
vv    DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  NO                             5                             22
  YES                           26                            123
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(17Q25.3) MUTATED                                  3     3
  DEL PEAK 26(17Q25.3) WILD-TYPE                                4    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(17Q25.3) MUTATED                           2
  DEL PEAK 26(17Q25.3) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 26(17Q25.3) MUTATED                                           1
  DEL PEAK 26(17Q25.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 26(17Q25.3) MUTATED      22
  DEL PEAK 26(17Q25.3) WILD-TYPE   108
D49V10, multiclass
                                           clus
vv                                          DEL PEAK 26(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               22
                                           clus
vv                                          DEL PEAK 26(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D49V11, binary
                                cls
clus                               0   1
  DEL PEAK 26(17Q25.3) MUTATED     2  22
  DEL PEAK 26(17Q25.3) WILD-TYPE   9 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17Q25.3) MUTATED      2   22
  DEL PEAK 26(17Q25.3) WILD-TYPE    9  105
                        clus
vv                       DEL PEAK 26(17Q25.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           22
                        clus
vv                       DEL PEAK 26(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            105
[1] 2 2
[1] FALSE
D49V12, continuous
D49V13, binary
                                cls
clus                              0  1
  DEL PEAK 26(17Q25.3) MUTATED    6  3
  DEL PEAK 26(17Q25.3) WILD-TYPE 42 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17Q25.3) MUTATED      6    3
  DEL PEAK 26(17Q25.3) WILD-TYPE   42   16
            clus
vv           DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  TUMOR FREE                            6                             42
  WITH TUMOR                            3                             16
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 26(17Q25.3) MUTATED         0      2       0            26       3
  DEL PEAK 26(17Q25.3) WILD-TYPE       1      8       6           121       9
D49V14, multiclass
               clus
vv              DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  0                              6
  UNITED STATES                           26                            121
  VIETNAM                                  3                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 26(17Q25.3) MUTATED    1 12 18  0  0
  DEL PEAK 26(17Q25.3) WILD-TYPE 13 71 54  1  5
D49V15, multiclass
    clus
vv   DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  G1                            1                             13
  G2                           12                             71
  G3                           18                             54
  G4                            0                              1
  GX                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V16, continuous
[1] "Remove cluster labels:"       "DEL PEAK 26(17Q25.3) MUTATED"
clus
  DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE 
                             2                             23 
                    TCGA-BI-A0VR                     TCGA-C5-A1BJ 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-C5-A1BL                     TCGA-C5-A1BQ 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-C5-A1ME                     TCGA-C5-A1MF 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-C5-A2M2                     TCGA-C5-A3HD 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-C5-A7CM                     TCGA-C5-A7CO 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-DS-A3LQ                     TCGA-EX-A69M 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-FU-A2QG                     TCGA-FU-A3TX 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-FU-A3WB                     TCGA-HM-A3JK 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-IR-A3L7                     TCGA-IR-A3LB 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-IR-A3LH                     TCGA-MU-A5YI 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-MU-A8JM                     TCGA-Q1-A6DW 
"DEL PEAK 26(17Q25.3) WILD-TYPE" "DEL PEAK 26(17Q25.3) WILD-TYPE" 
                    TCGA-RA-A741 
"DEL PEAK 26(17Q25.3) WILD-TYPE" 
D49V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 26(17Q25.3) MUTATED                                             1
  DEL PEAK 26(17Q25.3) WILD-TYPE                                          20
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 26(17Q25.3) MUTATED                                        2
  DEL PEAK 26(17Q25.3) WILD-TYPE                                      6
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 26(17Q25.3) MUTATED                                                 0
  DEL PEAK 26(17Q25.3) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 26(17Q25.3) MUTATED                8                  10
  DEL PEAK 26(17Q25.3) WILD-TYPE             28                  73
D49V18, multiclass
                                                 clus
vv                                                DEL PEAK 26(17Q25.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             8
  LIFELONG NON-SMOKER                                                       10
                                                 clus
vv                                                DEL PEAK 26(17Q25.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              28
  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"
D49V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 26(17Q25.3) MUTATED             3        5             3        1
  DEL PEAK 26(17Q25.3) WILD-TYPE          14       32             8        4
D49V20, multiclass
               clus
vv              DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  COMBINATION                              3                             14
  EXTERNAL                                 5                             32
  EXTERNAL BEAM                            3                              8
  INTERNAL                                 1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V21, binary
                                cls
clus                              0  1
  DEL PEAK 26(17Q25.3) MUTATED    1  0
  DEL PEAK 26(17Q25.3) WILD-TYPE 10  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17Q25.3) MUTATED      1    0
  DEL PEAK 26(17Q25.3) WILD-TYPE   10    3
     clus
vv    DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  CGY                            1                             10
  GY                             0                              3
[1] 2 2
[1] FALSE
D49V22, continuous
D49V23, continuous
D49V24, continuous
D49V25, continuous
D49V26, continuous
D49V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 26(17Q25.3) MUTATED                                     0
  DEL PEAK 26(17Q25.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 26(17Q25.3) MUTATED                                     1
  DEL PEAK 26(17Q25.3) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 26(17Q25.3) MUTATED                         3
  DEL PEAK 26(17Q25.3) WILD-TYPE                       6
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 26(17Q25.3) MUTATED                         0
  DEL PEAK 26(17Q25.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 26(17Q25.3) MUTATED                         1
  DEL PEAK 26(17Q25.3) WILD-TYPE                       4
D49V28, multiclass
                                     clus
vv                                    DEL PEAK 26(17Q25.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        3
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 26(17Q25.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          6
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 26(17Q25.3) MUTATED                                               0
  DEL PEAK 26(17Q25.3) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 26(17Q25.3) MUTATED                                                1
  DEL PEAK 26(17Q25.3) WILD-TYPE                                              9
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 26(17Q25.3) MUTATED                                                                                   9
  DEL PEAK 26(17Q25.3) WILD-TYPE                                                                                45
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 26(17Q25.3) MUTATED                                                                                             13
  DEL PEAK 26(17Q25.3) WILD-TYPE                                                                                           64
D49V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 26(17Q25.3) 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)                           13
                                                                                              clus
vv                                                                                             DEL PEAK 26(17Q25.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V30, binary
                                cls
clus                              0  1
  DEL PEAK 26(17Q25.3) MUTATED    8 10
  DEL PEAK 26(17Q25.3) WILD-TYPE 46 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17Q25.3) MUTATED      8   10
  DEL PEAK 26(17Q25.3) WILD-TYPE   46   49
         clus
vv        DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  ABSENT                             8                             46
  PRESENT                           10                             49
[1] 2 2
[1] FALSE
D49V31, continuous
D49V32, continuous
D49V33, binary
                                cls
clus                              0  1
  DEL PEAK 26(17Q25.3) MUTATED    9 13
  DEL PEAK 26(17Q25.3) WILD-TYPE 26 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17Q25.3) MUTATED      9   13
  DEL PEAK 26(17Q25.3) WILD-TYPE   26   68
                                          clus
vv                                         DEL PEAK 26(17Q25.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           13
                                          clus
vv                                         DEL PEAK 26(17Q25.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             68
[1] 2 2
[1] FALSE
D49V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 26(17Q25.3) MUTATED       0                   22                   1
  DEL PEAK 26(17Q25.3) WILD-TYPE     3                   91                   4
D49V35, multiclass
                      clus
vv                     DEL PEAK 26(17Q25.3) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           22
  SIMPLE HYSTERECTOMY                             1
                      clus
vv                     DEL PEAK 26(17Q25.3) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             91
  SIMPLE HYSTERECTOMY                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 26(17Q25.3) MUTATED              2           6          6
  DEL PEAK 26(17Q25.3) WILD-TYPE            6          34         34
D49V36, multiclass
              clus
vv             DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                             6                             34
  NEVER USED                              6                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V37, continuous
D49V38, binary
                                cls
clus                              0  1
  DEL PEAK 26(17Q25.3) MUTATED    9  1
  DEL PEAK 26(17Q25.3) WILD-TYPE 64 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17Q25.3) MUTATED      9    1
  DEL PEAK 26(17Q25.3) WILD-TYPE   64   13
         clus
vv        DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  ABSENT                             9                             64
  PRESENT                            1                             13
[1] 2 2
[1] FALSE
D49V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 26(17Q25.3) MUTATED     1    0   4    8    6  0   2    1    0   3
  DEL PEAK 26(17Q25.3) WILD-TYPE   1    1  18   43   15  3   4    5    8  10
                                vv
clus                             T3B T4 TX
  DEL PEAK 26(17Q25.3) MUTATED     0  0  0
  DEL PEAK 26(17Q25.3) WILD-TYPE   2  1  7
D49V40, multiclass
      clus
vv     DEL PEAK 26(17Q25.3) MUTATED DEL PEAK 26(17Q25.3) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             4                             18
  T1B1                            8                             43
  T1B2                            6                             15
  T2                              0                              3
  T2A                             2                              4
  T2A1                            1                              5
  T2A2                            0                              8
  T2B                             3                             10
  T3B                             0                              2
  T4                              0                              1
  TX                              0                              7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V41, continuous

Clustering(50) Variable = DEL PEAK 27(18Q21.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(18Q21.2) MUTATED    37  10
  DEL PEAK 27(18Q21.2) WILD-TYPE 100  22
  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE 
                            47                            122 
  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE 
                            10                             22 
$`DEL PEAK 27(18Q21.2) MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MN 
       31.40        35.01        57.73        35.61         0.46        40.93 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A7CH 
       73.18        73.45        78.35        38.43         0.82        25.35 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VN 
       17.19        60.69        13.61         2.73        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-A2IP TCGA-EK-A2PG TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EX-A1H6 TCGA-EX-A3L1 
        6.64         0.53        23.70         2.24         7.92         6.94 
TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LH 
        2.17         1.12        21.67       137.16        66.81        78.71 
TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A4AX TCGA-Q1-A5R1 
       81.96        16.64        10.06         0.89         0.07         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73P TCGA-RA-A741 TCGA-UC-A7PD 
        3.45         3.39         4.80         3.88        11.67 

$`DEL PEAK 27(18Q21.2) 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-A2LX TCGA-C5-A2LZ TCGA-C5-A3HD 
        2.43         3.58        44.22        83.05       100.14        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       15.48         9.67        73.41        85.55        94.95         9.34 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18         7.33         8.28         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50        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-EK-A2R7 
        0.69        14.99        14.96        13.58        13.48         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RN 
        0.07         4.04         0.03         0.36         1.18         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A449 
        0.07         0.10         0.10         0.03        20.35        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY 
        4.47         6.12         1.22        23.84         0.92         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-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.35         1.32         1.97        25.41        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LK TCGA-IR-A3LL 
        4.11       147.39       117.40        96.95        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU 
       14.43        19.33        20.48        15.58         5.13         0.10 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73R 
        4.34         2.96         5.85         3.72         5.75         6.25 
TCGA-R2-A69V TCGA-UC-A7PF 
       19.59        93.99 

  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE 
                        137.16                         182.93 
  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE 
                         13.61                          13.53 
[1] "0.1 - 137.2 (13.6)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.1"
D50V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 27(18Q21.2) MUTATED   26        8
  DEL PEAK 27(18Q21.2) WILD-TYPE 71       31
D50V3, multiclass
          clus
vv         DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  T1                                 26                             71
  T2+T3+T4                            8                             31
[1] 2 2
[1] FALSE
D50V4, binary
                                cls
clus                              0  1
  DEL PEAK 27(18Q21.2) MUTATED   24  8
  DEL PEAK 27(18Q21.2) WILD-TYPE 63 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(18Q21.2) MUTATED     24    8
  DEL PEAK 27(18Q21.2) WILD-TYPE   63   32
   clus
vv  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  0                           24                             63
  1                            8                             32
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 27(18Q21.2) MUTATED   20  1 15
  DEL PEAK 27(18Q21.2) WILD-TYPE 52  2 50
D50V5, multiclass
    clus
vv   DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  M0                           20                             52
  M1                            1                              2
  MX                           15                             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(18Q21.2) MUTATED               0                               32
  DEL PEAK 27(18Q21.2) WILD-TYPE             2                              112
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 27(18Q21.2) MUTATED                                               1
  DEL PEAK 27(18Q21.2) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 27(18Q21.2) MUTATED                                    13
  DEL PEAK 27(18Q21.2) WILD-TYPE                                   7
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 27(18Q21.2) MUTATED                                           2
  DEL PEAK 27(18Q21.2) WILD-TYPE                                         0
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 27(18Q21.2) MUTATED                                              2
  DEL PEAK 27(18Q21.2) WILD-TYPE                                            2
D50V6, multiclass
                                               clus
vv                                              DEL PEAK 27(18Q21.2) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        32
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             2
                                               clus
vv                                              DEL PEAK 27(18Q21.2) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         112
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(18Q21.2) MUTATED     8  42
  DEL PEAK 27(18Q21.2) WILD-TYPE  19 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(18Q21.2) MUTATED      8   42
  DEL PEAK 27(18Q21.2) WILD-TYPE   19  107
     clus
vv    DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  NO                             8                             19
  YES                           42                            107
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(18Q21.2) MUTATED                                  2     3
  DEL PEAK 27(18Q21.2) WILD-TYPE                                5    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(18Q21.2) MUTATED                           7
  DEL PEAK 27(18Q21.2) WILD-TYPE                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(18Q21.2) MUTATED                                           0
  DEL PEAK 27(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 27(18Q21.2) MUTATED      38
  DEL PEAK 27(18Q21.2) WILD-TYPE    92
D50V10, multiclass
                                           clus
vv                                          DEL PEAK 27(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               38
                                           clus
vv                                          DEL PEAK 27(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                 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"
D50V11, binary
                                cls
clus                              0  1
  DEL PEAK 27(18Q21.2) MUTATED    3 35
  DEL PEAK 27(18Q21.2) WILD-TYPE  8 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(18Q21.2) MUTATED      3   35
  DEL PEAK 27(18Q21.2) WILD-TYPE    8   92
                        clus
vv                       DEL PEAK 27(18Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       DEL PEAK 27(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             92
[1] 2 2
[1] FALSE
D50V12, continuous
D50V13, binary
                                cls
clus                              0  1
  DEL PEAK 27(18Q21.2) MUTATED   14  4
  DEL PEAK 27(18Q21.2) WILD-TYPE 34 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(18Q21.2) MUTATED     14    4
  DEL PEAK 27(18Q21.2) WILD-TYPE   34   15
            clus
vv           DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  TUMOR FREE                           14                             34
  WITH TUMOR                            4                             15
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 27(18Q21.2) MUTATED         0      3       1            44       2
  DEL PEAK 27(18Q21.2) WILD-TYPE       1      7       5           103      10
D50V14, multiclass
               clus
vv              DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   3                              7
  UKRAINE                                  1                              5
  UNITED STATES                           44                            103
  VIETNAM                                  2                             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 27(18Q21.2) MUTATED    4 20 22  1  3
  DEL PEAK 27(18Q21.2) WILD-TYPE 10 63 50  0  2
D50V15, multiclass
    clus
vv   DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  G1                            4                             10
  G2                           20                             63
  G3                           22                             50
  G4                            1                              0
  GX                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V16, continuous
D50V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 27(18Q21.2) MUTATED                                             4
  DEL PEAK 27(18Q21.2) WILD-TYPE                                          17
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 27(18Q21.2) MUTATED                                        1
  DEL PEAK 27(18Q21.2) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 27(18Q21.2) MUTATED                                                 0
  DEL PEAK 27(18Q21.2) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 27(18Q21.2) MUTATED               10                  24
  DEL PEAK 27(18Q21.2) WILD-TYPE             26                  59
D50V18, multiclass
                                                 clus
vv                                                DEL PEAK 27(18Q21.2) 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                                                       24
                                                 clus
vv                                                DEL PEAK 27(18Q21.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              26
  LIFELONG NON-SMOKER                                                         59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 27(18Q21.2) MUTATED             4        9             4        3
  DEL PEAK 27(18Q21.2) WILD-TYPE          13       28             7        2
D50V20, multiclass
               clus
vv              DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  COMBINATION                              4                             13
  EXTERNAL                                 9                             28
  EXTERNAL BEAM                            4                              7
  INTERNAL                                 3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V21, binary
                                cls
clus                             0 1
  DEL PEAK 27(18Q21.2) MUTATED   3 1
  DEL PEAK 27(18Q21.2) WILD-TYPE 8 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(18Q21.2) MUTATED      3    1
  DEL PEAK 27(18Q21.2) WILD-TYPE    8    2
     clus
vv    DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  CGY                            3                              8
  GY                             1                              2
[1] 2 2
[1] FALSE
D50V22, continuous
D50V23, continuous
D50V24, continuous
D50V25, continuous
D50V26, continuous
D50V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 27(18Q21.2) MUTATED                                     0
  DEL PEAK 27(18Q21.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 27(18Q21.2) MUTATED                                     1
  DEL PEAK 27(18Q21.2) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 27(18Q21.2) MUTATED                         2
  DEL PEAK 27(18Q21.2) WILD-TYPE                       7
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 27(18Q21.2) MUTATED                         0
  DEL PEAK 27(18Q21.2) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 27(18Q21.2) MUTATED                         2
  DEL PEAK 27(18Q21.2) WILD-TYPE                       3
D50V28, multiclass
                                     clus
vv                                    DEL PEAK 27(18Q21.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        2
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 27(18Q21.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          7
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 27(18Q21.2) MUTATED                                               0
  DEL PEAK 27(18Q21.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 27(18Q21.2) MUTATED                                                4
  DEL PEAK 27(18Q21.2) WILD-TYPE                                              6
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 27(18Q21.2) MUTATED                                                                                  15
  DEL PEAK 27(18Q21.2) WILD-TYPE                                                                                39
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 27(18Q21.2) MUTATED                                                                                             22
  DEL PEAK 27(18Q21.2) WILD-TYPE                                                                                           55
D50V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 27(18Q21.2) 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)                           22
                                                                                              clus
vv                                                                                             DEL PEAK 27(18Q21.2) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        39
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V30, binary
                                cls
clus                              0  1
  DEL PEAK 27(18Q21.2) MUTATED   18 10
  DEL PEAK 27(18Q21.2) WILD-TYPE 36 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(18Q21.2) MUTATED     18   10
  DEL PEAK 27(18Q21.2) WILD-TYPE   36   49
         clus
vv        DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  ABSENT                            18                             36
  PRESENT                           10                             49
[1] 2 2
[1] FALSE
D50V31, continuous
D50V32, continuous
D50V33, binary
                                cls
clus                              0  1
  DEL PEAK 27(18Q21.2) MUTATED    9 18
  DEL PEAK 27(18Q21.2) WILD-TYPE 26 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(18Q21.2) MUTATED      9   18
  DEL PEAK 27(18Q21.2) WILD-TYPE   26   63
                                          clus
vv                                         DEL PEAK 27(18Q21.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           18
                                          clus
vv                                         DEL PEAK 27(18Q21.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             63
[1] 2 2
[1] FALSE
D50V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 27(18Q21.2) MUTATED       1                   28                   2
  DEL PEAK 27(18Q21.2) WILD-TYPE     2                   85                   3
D50V35, multiclass
                      clus
vv                     DEL PEAK 27(18Q21.2) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           28
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     DEL PEAK 27(18Q21.2) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             85
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 27(18Q21.2) MUTATED              4          17         10
  DEL PEAK 27(18Q21.2) WILD-TYPE            4          23         30
D50V36, multiclass
              clus
vv             DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  CURRENT USER                            4                              4
  FORMER USER                            17                             23
  NEVER USED                             10                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V37, continuous
D50V38, binary
                                cls
clus                              0  1
  DEL PEAK 27(18Q21.2) MUTATED   24  1
  DEL PEAK 27(18Q21.2) WILD-TYPE 49 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(18Q21.2) MUTATED     24    1
  DEL PEAK 27(18Q21.2) WILD-TYPE   49   13
         clus
vv        DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  ABSENT                            24                             49
  PRESENT                            1                             13
[1] 2 2
[1] FALSE
D50V39, continuous
[1] "Remove cluster labels:"       "DEL PEAK 27(18Q21.2) MUTATED"
clus
  DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE 
                             1                              8 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 27(18Q21.2) WILD-TYPE" "DEL PEAK 27(18Q21.2) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK 27(18Q21.2) WILD-TYPE" "DEL PEAK 27(18Q21.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 27(18Q21.2) WILD-TYPE" "DEL PEAK 27(18Q21.2) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 27(18Q21.2) WILD-TYPE" "DEL PEAK 27(18Q21.2) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 27(18Q21.2) MUTATED     1    0   6   17    2  0   1    2    1   3
  DEL PEAK 27(18Q21.2) WILD-TYPE   1    1  16   34   19  3   5    4    7  10
                                vv
clus                             T3B T4 TX
  DEL PEAK 27(18Q21.2) MUTATED     1  0  2
  DEL PEAK 27(18Q21.2) WILD-TYPE   1  1  5
D50V40, multiclass
      clus
vv     DEL PEAK 27(18Q21.2) MUTATED DEL PEAK 27(18Q21.2) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             6                             16
  T1B1                           17                             34
  T1B2                            2                             19
  T2                              0                              3
  T2A                             1                              5
  T2A1                            2                              4
  T2A2                            1                              7
  T2B                             3                             10
  T3B                             1                              1
  T4                              0                              1
  TX                              2                              5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V41, continuous

Clustering(51) Variable = DEL PEAK 28(19P13.3) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(19P13.3) MUTATED   39 12
  DEL PEAK 28(19P13.3) WILD-TYPE 98 20
  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE 
                            51                            118 
  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE 
                            12                             20 
$`DEL PEAK 28(19P13.3) MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 
       23.67        11.44        18.74         5.46        31.40        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MN 
       35.01        57.73        53.16        35.61         0.46        40.93 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7X3 TCGA-C5-A7X5 
       52.01        18.02        15.48        73.41         9.34        13.61 
TCGA-C5-A7X8 TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI 
        2.73       117.99       118.65        16.83         7.33         8.28 
TCGA-EA-A1QT TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 
       12.36        14.50         1.35        14.50         1.81        13.91 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RJ 
       14.99        14.96        13.58         6.64         0.59         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A69L TCGA-FU-A23L 
        2.24         0.10         0.10         0.03         4.47        23.84 
TCGA-FU-A5XV TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-JW-A5VI TCGA-JW-A5VK TCGA-LP-A4AX 
        1.97        14.93       117.40        16.64        20.48         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-RA-A741 
        2.96         5.85         3.88 

$`DEL PEAK 28(19P13.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        57.04        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1MH 
      173.29        82.85        19.86        67.46        46.32        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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14        38.43         0.82        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7UC 
      182.93        25.35       101.82       134.33         9.67        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       85.55        60.69        94.95        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
        2.66        22.98        16.18         0.76         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S 
        0.82         0.62        13.05         1.18         1.35        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A78R 
       12.82         0.26        14.89         1.48         0.69        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       12.59        45.96         0.53         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.36        23.70         0.07         0.10        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        6.94        14.70         6.12         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.66         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        3.52         1.35         1.32         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       20.78         4.11       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-A5VJ 
       78.71        81.96        26.56        36.36        14.43        19.33 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 
       15.58        10.06         5.13         0.10         0.89         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.72         3.45         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        19.59        11.67        93.99 

  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE 
                        118.65                         182.93 
  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE 
                        13.910                         12.935 
[1] "0.0 - 118.7 (13.9)" "0.0 - 182.9 (12.9)"
[1] "hr=" "1.9"
D51V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 28(19P13.3) MUTATED   30        8
  DEL PEAK 28(19P13.3) WILD-TYPE 67       31
D51V3, multiclass
          clus
vv         DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  T1                                 30                             67
  T2+T3+T4                            8                             31
[1] 2 2
[1] FALSE
D51V4, binary
                                cls
clus                              0  1
  DEL PEAK 28(19P13.3) MUTATED   25 11
  DEL PEAK 28(19P13.3) WILD-TYPE 62 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(19P13.3) MUTATED     25   11
  DEL PEAK 28(19P13.3) WILD-TYPE   62   29
   clus
vv  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  0                           25                             62
  1                           11                             29
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 28(19P13.3) MUTATED   22  0 17
  DEL PEAK 28(19P13.3) WILD-TYPE 50  3 48
D51V5, multiclass
    clus
vv   DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  M0                           22                             50
  M1                            0                              3
  MX                           17                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(19P13.3) MUTATED               0                               49
  DEL PEAK 28(19P13.3) WILD-TYPE             2                               95
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 28(19P13.3) MUTATED                                               0
  DEL PEAK 28(19P13.3) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 28(19P13.3) MUTATED                                     5
  DEL PEAK 28(19P13.3) WILD-TYPE                                  15
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 28(19P13.3) MUTATED                                           0
  DEL PEAK 28(19P13.3) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 28(19P13.3) MUTATED                                              1
  DEL PEAK 28(19P13.3) WILD-TYPE                                            3
D51V6, multiclass
                                               clus
vv                                              DEL PEAK 28(19P13.3) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             1
                                               clus
vv                                              DEL PEAK 28(19P13.3) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          95
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       15
  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"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(19P13.3) MUTATED    10  45
  DEL PEAK 28(19P13.3) WILD-TYPE  17 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(19P13.3) MUTATED     10   45
  DEL PEAK 28(19P13.3) WILD-TYPE   17  104
     clus
vv    DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  NO                            10                             17
  YES                           45                            104
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(19P13.3) MUTATED                                  1     6
  DEL PEAK 28(19P13.3) WILD-TYPE                                6     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(19P13.3) MUTATED                           4
  DEL PEAK 28(19P13.3) WILD-TYPE                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 28(19P13.3) MUTATED                                           1
  DEL PEAK 28(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 28(19P13.3) MUTATED      43
  DEL PEAK 28(19P13.3) WILD-TYPE    87
D51V10, multiclass
                                           clus
vv                                          DEL PEAK 28(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               43
                                           clus
vv                                          DEL PEAK 28(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, binary
                                cls
clus                              0  1
  DEL PEAK 28(19P13.3) MUTATED    2 42
  DEL PEAK 28(19P13.3) WILD-TYPE  9 85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(19P13.3) MUTATED      2   42
  DEL PEAK 28(19P13.3) WILD-TYPE    9   85
                        clus
vv                       DEL PEAK 28(19P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       DEL PEAK 28(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                             85
[1] 2 2
[1] FALSE
D51V12, continuous
D51V13, binary
                                cls
clus                              0  1
  DEL PEAK 28(19P13.3) MUTATED   19  8
  DEL PEAK 28(19P13.3) WILD-TYPE 29 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(19P13.3) MUTATED     19    8
  DEL PEAK 28(19P13.3) WILD-TYPE   29   11
            clus
vv           DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  TUMOR FREE                           19                             29
  WITH TUMOR                            8                             11
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 28(19P13.3) MUTATED         1      2       3            44       5
  DEL PEAK 28(19P13.3) WILD-TYPE       0      8       3           103       7
D51V14, multiclass
               clus
vv              DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  NIGERIA                                  1                              0
  RUSSIA                                   2                              8
  UKRAINE                                  3                              3
  UNITED STATES                           44                            103
  VIETNAM                                  5                              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 28(19P13.3) MUTATED    2 23 28  0  1
  DEL PEAK 28(19P13.3) WILD-TYPE 12 60 44  1  4
D51V15, multiclass
    clus
vv   DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  G1                            2                             12
  G2                           23                             60
  G3                           28                             44
  G4                            0                              1
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V16, continuous
D51V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 28(19P13.3) MUTATED                                             4
  DEL PEAK 28(19P13.3) WILD-TYPE                                          17
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 28(19P13.3) MUTATED                                        3
  DEL PEAK 28(19P13.3) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 28(19P13.3) MUTATED                                                 0
  DEL PEAK 28(19P13.3) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 28(19P13.3) MUTATED                9                  26
  DEL PEAK 28(19P13.3) WILD-TYPE             27                  57
D51V18, multiclass
                                                 clus
vv                                                DEL PEAK 28(19P13.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             9
  LIFELONG NON-SMOKER                                                       26
                                                 clus
vv                                                DEL PEAK 28(19P13.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              27
  LIFELONG NON-SMOKER                                                         57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 28(19P13.3) MUTATED             6       15             4        3
  DEL PEAK 28(19P13.3) WILD-TYPE          11       22             7        2
D51V20, multiclass
               clus
vv              DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  COMBINATION                              6                             11
  EXTERNAL                                15                             22
  EXTERNAL BEAM                            4                              7
  INTERNAL                                 3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V21, binary
                                cls
clus                             0 1
  DEL PEAK 28(19P13.3) MUTATED   4 2
  DEL PEAK 28(19P13.3) WILD-TYPE 7 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(19P13.3) MUTATED      4    2
  DEL PEAK 28(19P13.3) WILD-TYPE    7    1
     clus
vv    DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  CGY                            4                              7
  GY                             2                              1
[1] 2 2
[1] FALSE
D51V22, continuous
D51V23, continuous
D51V24, continuous
D51V25, continuous
D51V26, continuous
D51V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 28(19P13.3) MUTATED                                     0
  DEL PEAK 28(19P13.3) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 28(19P13.3) MUTATED                                     2
  DEL PEAK 28(19P13.3) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 28(19P13.3) MUTATED                         4
  DEL PEAK 28(19P13.3) WILD-TYPE                       5
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 28(19P13.3) MUTATED                         0
  DEL PEAK 28(19P13.3) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 28(19P13.3) MUTATED                         0
  DEL PEAK 28(19P13.3) WILD-TYPE                       5
D51V28, multiclass
                                     clus
vv                                    DEL PEAK 28(19P13.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        4
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        0
                                     clus
vv                                    DEL PEAK 28(19P13.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                          5
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 28(19P13.3) MUTATED                                               1
  DEL PEAK 28(19P13.3) WILD-TYPE                                             1
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 28(19P13.3) MUTATED                                                5
  DEL PEAK 28(19P13.3) WILD-TYPE                                              5
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 28(19P13.3) MUTATED                                                                                  11
  DEL PEAK 28(19P13.3) WILD-TYPE                                                                                43
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 28(19P13.3) MUTATED                                                                                             22
  DEL PEAK 28(19P13.3) WILD-TYPE                                                                                           55
D51V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 28(19P13.3) 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)                           22
                                                                                              clus
vv                                                                                             DEL PEAK 28(19P13.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        43
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V30, binary
                                cls
clus                              0  1
  DEL PEAK 28(19P13.3) MUTATED   13 20
  DEL PEAK 28(19P13.3) WILD-TYPE 41 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(19P13.3) MUTATED     13   20
  DEL PEAK 28(19P13.3) WILD-TYPE   41   39
         clus
vv        DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  ABSENT                            13                             41
  PRESENT                           20                             39
[1] 2 2
[1] FALSE
D51V31, continuous
D51V32, continuous
D51V33, binary
                                cls
clus                              0  1
  DEL PEAK 28(19P13.3) MUTATED   11 25
  DEL PEAK 28(19P13.3) WILD-TYPE 24 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(19P13.3) MUTATED     11   25
  DEL PEAK 28(19P13.3) WILD-TYPE   24   56
                                          clus
vv                                         DEL PEAK 28(19P13.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           25
                                          clus
vv                                         DEL PEAK 28(19P13.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             56
[1] 2 2
[1] FALSE
D51V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 28(19P13.3) MUTATED       0                   34                   2
  DEL PEAK 28(19P13.3) WILD-TYPE     3                   79                   3
D51V35, multiclass
                      clus
vv                     DEL PEAK 28(19P13.3) MUTATED
  OTHER                                           0
  RADICAL HYSTERECTOMY                           34
  SIMPLE HYSTERECTOMY                             2
                      clus
vv                     DEL PEAK 28(19P13.3) WILD-TYPE
  OTHER                                             3
  RADICAL HYSTERECTOMY                             79
  SIMPLE HYSTERECTOMY                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 28(19P13.3) MUTATED              2          16          9
  DEL PEAK 28(19P13.3) WILD-TYPE            6          24         31
D51V36, multiclass
              clus
vv             DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                            16                             24
  NEVER USED                              9                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V37, continuous
D51V38, binary
                                cls
clus                              0  1
  DEL PEAK 28(19P13.3) MUTATED   22  3
  DEL PEAK 28(19P13.3) WILD-TYPE 51 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(19P13.3) MUTATED     22    3
  DEL PEAK 28(19P13.3) WILD-TYPE   51   11
         clus
vv        DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  ABSENT                            22                             51
  PRESENT                            3                             11
[1] 2 2
[1] FALSE
D51V39, continuous
[1] "Remove cluster labels:"       "DEL PEAK 28(19P13.3) MUTATED"
clus
  DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1MH                     TCGA-C5-A1MP 
"DEL PEAK 28(19P13.3) WILD-TYPE" "DEL PEAK 28(19P13.3) WILD-TYPE" 
                    TCGA-EK-A2RO                     TCGA-HM-A3JK 
"DEL PEAK 28(19P13.3) WILD-TYPE" "DEL PEAK 28(19P13.3) WILD-TYPE" 
                    TCGA-JW-A852                     TCGA-MU-A51Y 
"DEL PEAK 28(19P13.3) WILD-TYPE" "DEL PEAK 28(19P13.3) WILD-TYPE" 
                    TCGA-MU-A8JM 
"DEL PEAK 28(19P13.3) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 28(19P13.3) MUTATED     0    0   4   18    8  0   1    2    1   3
  DEL PEAK 28(19P13.3) WILD-TYPE   2    1  18   33   13  3   5    4    7  10
                                vv
clus                             T3B T4 TX
  DEL PEAK 28(19P13.3) MUTATED     1  0  3
  DEL PEAK 28(19P13.3) WILD-TYPE   1  1  4
D51V40, multiclass
      clus
vv     DEL PEAK 28(19P13.3) MUTATED DEL PEAK 28(19P13.3) WILD-TYPE
  T1A                             0                              2
  T1A1                            0                              1
  T1B                             4                             18
  T1B1                           18                             33
  T1B2                            8                             13
  T2                              0                              3
  T2A                             1                              5
  T2A1                            2                              4
  T2A2                            1                              7
  T2B                             3                             10
  T3B                             1                              1
  T4                              0                              1
  TX                              3                              4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V41, continuous

Clustering(52) Variable = DEL PEAK 29(19Q13.33) MUTATION ANALYSIS
D52V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 29(19Q13.33) MUTATED    17   3
  DEL PEAK 29(19Q13.33) WILD-TYPE 120  29
  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE 
                             20                             149 
  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE 
                              3                              29 
$`DEL PEAK 29(19Q13.33) MUTATED`
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A7CM TCGA-C5-A7UI TCGA-C5-A7X8 
       30.21        35.01         0.46         9.67        94.95         2.73 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A556 TCGA-EK-A2IP TCGA-EK-A3GJ 
      118.65        12.36         1.32        14.89         6.64         0.10 
TCGA-FU-A3NI TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VI TCGA-JW-A5VK 
        1.45       117.40        78.71        81.96        16.64        20.48 
TCGA-MY-A5BD TCGA-Q1-A6DT 
       29.72         3.39 

$`DEL PEAK 29(19Q13.33) 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-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         2.43        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-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-A7CO TCGA-C5-A7UC 
       25.35       101.82       134.33        15.48        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       85.55        60.69         9.34        13.61        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
        7.33         8.28         0.76         1.74         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-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-EK-A2GZ 
        0.69        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       45.96         0.53         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-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-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         4.11       147.39       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VL 
       96.95        26.56        36.36        14.43        19.33        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       13.87         0.03         5.42         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.72         3.45         5.85         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        19.59         3.88        11.67        93.99 

  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE 
                         118.65                          182.93 
  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE 
                         15.765                          13.480 
[1] "0.1 - 118.7 (15.8)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.6"
D52V2, continuous
                                 vv
clus                              T1 T2+T3+T4
  DEL PEAK 29(19Q13.33) MUTATED   11        7
  DEL PEAK 29(19Q13.33) WILD-TYPE 86       32
D52V3, multiclass
          clus
vv         DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  T1                                  11                              86
  T2+T3+T4                             7                              32
[1] 2 2
[1] FALSE
D52V4, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.33) MUTATED   12  4
  DEL PEAK 29(19Q13.33) WILD-TYPE 75 36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.33) MUTATED     12    4
  DEL PEAK 29(19Q13.33) WILD-TYPE   75   36
   clus
vv  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  0                            12                              75
  1                             4                              36
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 29(19Q13.33) MUTATED    9  1  8
  DEL PEAK 29(19Q13.33) WILD-TYPE 63  2 57
D52V5, multiclass
    clus
vv   DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  M0                             9                              63
  M1                             1                               2
  MX                             8                              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 29(19Q13.33) MUTATED               0
  DEL PEAK 29(19Q13.33) WILD-TYPE             2
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(19Q13.33) MUTATED                                 15
  DEL PEAK 29(19Q13.33) WILD-TYPE                              129
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 29(19Q13.33) MUTATED                                               1
  DEL PEAK 29(19Q13.33) WILD-TYPE                                             3
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 29(19Q13.33) MUTATED                                     3
  DEL PEAK 29(19Q13.33) WILD-TYPE                                  17
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 29(19Q13.33) MUTATED                                           1
  DEL PEAK 29(19Q13.33) WILD-TYPE                                         1
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 29(19Q13.33) MUTATED                                              1
  DEL PEAK 29(19Q13.33) WILD-TYPE                                            3
D52V6, multiclass
                                               clus
vv                                              DEL PEAK 29(19Q13.33) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         15
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                              1
                                               clus
vv                                              DEL PEAK 29(19Q13.33) WILD-TYPE
  ADENOSQUAMOUS                                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          129
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   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"
D52V7, binary
                                 cls
clus                                0   1
  DEL PEAK 29(19Q13.33) MUTATED     3  18
  DEL PEAK 29(19Q13.33) WILD-TYPE  24 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.33) MUTATED      3   18
  DEL PEAK 29(19Q13.33) WILD-TYPE   24  131
     clus
vv    DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  NO                              3                              24
  YES                            18                             131
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(19Q13.33) MUTATED                                  1     0
  DEL PEAK 29(19Q13.33) WILD-TYPE                                6    15
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(19Q13.33) MUTATED                           3
  DEL PEAK 29(19Q13.33) WILD-TYPE                        15
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(19Q13.33) MUTATED                                           1
  DEL PEAK 29(19Q13.33) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 29(19Q13.33) MUTATED      16
  DEL PEAK 29(19Q13.33) WILD-TYPE   114
D52V10, multiclass
                                           clus
vv                                          DEL PEAK 29(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 0
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                16
                                           clus
vv                                          DEL PEAK 29(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        6
  ASIAN                                                                  15
  BLACK OR AFRICAN AMERICAN                                              15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 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"
D52V11, binary
                                 cls
clus                                0   1
  DEL PEAK 29(19Q13.33) MUTATED     3  11
  DEL PEAK 29(19Q13.33) WILD-TYPE   8 116
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.33) MUTATED      3   11
  DEL PEAK 29(19Q13.33) WILD-TYPE    8  116
                        clus
vv                       DEL PEAK 29(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            11
                        clus
vv                       DEL PEAK 29(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             116
[1] 2 2
[1] FALSE
D52V12, continuous
D52V13, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.33) MUTATED    8  1
  DEL PEAK 29(19Q13.33) WILD-TYPE 40 18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.33) MUTATED      8    1
  DEL PEAK 29(19Q13.33) WILD-TYPE   40   18
            clus
vv           DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  TUMOR FREE                             8                              40
  WITH TUMOR                             1                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 29(19Q13.33) MUTATED         0      3       0            18       0
  DEL PEAK 29(19Q13.33) WILD-TYPE       1      7       6           129      12
D52V14, multiclass
               clus
vv              DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  NIGERIA                                   0                               1
  RUSSIA                                    3                               7
  UKRAINE                                   0                               6
  UNITED STATES                            18                             129
  VIETNAM                                   0                              12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 29(19Q13.33) MUTATED    1  9  9  1  1
  DEL PEAK 29(19Q13.33) WILD-TYPE 13 74 63  0  4
D52V15, multiclass
    clus
vv   DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  G1                             1                              13
  G2                             9                              74
  G3                             9                              63
  G4                             1                               0
  GX                             1                               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V16, continuous
[1] "Remove cluster labels:"        "DEL PEAK 29(19Q13.33) MUTATED"
clus
  DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE 
                              2                              23 
                     TCGA-BI-A0VR                      TCGA-C5-A1BJ 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A1BL                      TCGA-C5-A1BQ 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A1ME                      TCGA-C5-A1MF 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A1MH                      TCGA-C5-A2M2 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-C5-A3HD                      TCGA-C5-A7CO 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-DS-A3LQ                      TCGA-EX-A69M 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-FU-A2QG                      TCGA-FU-A3TX 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-FU-A3WB                      TCGA-HM-A3JK 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-HM-A4S6                      TCGA-IR-A3L7 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-IR-A3LB                      TCGA-MU-A5YI 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-MU-A8JM                      TCGA-Q1-A6DW 
"DEL PEAK 29(19Q13.33) WILD-TYPE" "DEL PEAK 29(19Q13.33) WILD-TYPE" 
                     TCGA-RA-A741 
"DEL PEAK 29(19Q13.33) WILD-TYPE" 
D52V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 29(19Q13.33) MUTATED                                             2
  DEL PEAK 29(19Q13.33) WILD-TYPE                                          19
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 29(19Q13.33) MUTATED                                        1
  DEL PEAK 29(19Q13.33) WILD-TYPE                                      7
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 29(19Q13.33) MUTATED                                                 0
  DEL PEAK 29(19Q13.33) WILD-TYPE                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 29(19Q13.33) MUTATED                5                  10
  DEL PEAK 29(19Q13.33) WILD-TYPE             31                  73
D52V18, multiclass
                                                 clus
vv                                                DEL PEAK 29(19Q13.33) 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                                                        10
                                                 clus
vv                                                DEL PEAK 29(19Q13.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               31
  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"
D52V19, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 29(19Q13.33) MUTATED             0        6             3        0
  DEL PEAK 29(19Q13.33) WILD-TYPE          17       31             8        5
D52V20, multiclass
               clus
vv              DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  COMBINATION                               0                              17
  EXTERNAL                                  6                              31
  EXTERNAL BEAM                             3                               8
  INTERNAL                                  0                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V21, binary
                                 cls
clus                              0 1
  DEL PEAK 29(19Q13.33) MUTATED   2 0
  DEL PEAK 29(19Q13.33) WILD-TYPE 9 3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.33) MUTATED      2    0
  DEL PEAK 29(19Q13.33) WILD-TYPE    9    3
     clus
vv    DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  CGY                             2                               9
  GY                              0                               3
[1] 2 2
[1] FALSE
D52V22, continuous
D52V23, continuous
D52V24, continuous
D52V25, continuous
D52V26, continuous
D52V27, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 29(19Q13.33) MUTATED                                     0
  DEL PEAK 29(19Q13.33) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 29(19Q13.33) MUTATED                                     1
  DEL PEAK 29(19Q13.33) WILD-TYPE                                   5
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 29(19Q13.33) MUTATED                         1
  DEL PEAK 29(19Q13.33) WILD-TYPE                       8
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 29(19Q13.33) MUTATED                         0
  DEL PEAK 29(19Q13.33) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 29(19Q13.33) MUTATED                         1
  DEL PEAK 29(19Q13.33) WILD-TYPE                       4
D52V28, multiclass
                                     clus
vv                                    DEL PEAK 29(19Q13.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             1
  OTHER LOCATION, SPECIFY                                         1
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         1
                                     clus
vv                                    DEL PEAK 29(19Q13.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               5
  OTHER LOCATION, SPECIFY                                           8
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           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)
  DEL PEAK 29(19Q13.33) MUTATED                                               1
  DEL PEAK 29(19Q13.33) WILD-TYPE                                             1
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 29(19Q13.33) MUTATED                                                1
  DEL PEAK 29(19Q13.33) WILD-TYPE                                              9
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 29(19Q13.33) MUTATED                                                                                   6
  DEL PEAK 29(19Q13.33) WILD-TYPE                                                                                48
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 29(19Q13.33) MUTATED                                                                                              8
  DEL PEAK 29(19Q13.33) WILD-TYPE                                                                                           69
D52V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 29(19Q13.33) 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)                                        6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             8
                                                                                              clus
vv                                                                                             DEL PEAK 29(19Q13.33) 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)                                         48
  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"
D52V30, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.33) MUTATED    5  8
  DEL PEAK 29(19Q13.33) WILD-TYPE 49 51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.33) MUTATED      5    8
  DEL PEAK 29(19Q13.33) WILD-TYPE   49   51
         clus
vv        DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  ABSENT                              5                              49
  PRESENT                             8                              51
[1] 2 2
[1] FALSE
D52V31, continuous
D52V32, continuous
D52V33, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.33) MUTATED    4  7
  DEL PEAK 29(19Q13.33) WILD-TYPE 31 74
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.33) MUTATED      4    7
  DEL PEAK 29(19Q13.33) WILD-TYPE   31   74
                                          clus
vv                                         DEL PEAK 29(19Q13.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 4
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             7
                                          clus
vv                                         DEL PEAK 29(19Q13.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              74
[1] 2 2
[1] FALSE
D52V34, continuous
                                 vv
clus                              OTHER RADICAL HYSTERECTOMY
  DEL PEAK 29(19Q13.33) MUTATED       0                   15
  DEL PEAK 29(19Q13.33) WILD-TYPE     3                   98
                                 vv
clus                              SIMPLE HYSTERECTOMY
  DEL PEAK 29(19Q13.33) MUTATED                     0
  DEL PEAK 29(19Q13.33) WILD-TYPE                   5
D52V35, multiclass
                      clus
vv                     DEL PEAK 29(19Q13.33) MUTATED
  OTHER                                            0
  RADICAL HYSTERECTOMY                            15
  SIMPLE HYSTERECTOMY                              0
                      clus
vv                     DEL PEAK 29(19Q13.33) WILD-TYPE
  OTHER                                              3
  RADICAL HYSTERECTOMY                              98
  SIMPLE HYSTERECTOMY                                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 29(19Q13.33) MUTATED              1           4          6
  DEL PEAK 29(19Q13.33) WILD-TYPE            7          36         34
D52V36, multiclass
              clus
vv             DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  CURRENT USER                             1                               7
  FORMER USER                              4                              36
  NEVER USED                               6                              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V37, continuous
D52V38, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.33) MUTATED   11  1
  DEL PEAK 29(19Q13.33) WILD-TYPE 62 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.33) MUTATED     11    1
  DEL PEAK 29(19Q13.33) WILD-TYPE   62   13
         clus
vv        DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  ABSENT                             11                              62
  PRESENT                             1                              13
[1] 2 2
[1] FALSE
D52V39, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 29(19Q13.33) MUTATED     0    0   2    7    2  0   2    1    0   3
  DEL PEAK 29(19Q13.33) WILD-TYPE   2    1  20   44   19  3   4    5    8  10
                                 vv
clus                              T3B T4 TX
  DEL PEAK 29(19Q13.33) MUTATED     1  0  1
  DEL PEAK 29(19Q13.33) WILD-TYPE   1  1  6
D52V40, multiclass
      clus
vv     DEL PEAK 29(19Q13.33) MUTATED DEL PEAK 29(19Q13.33) WILD-TYPE
  T1A                              0                               2
  T1A1                             0                               1
  T1B                              2                              20
  T1B1                             7                              44
  T1B2                             2                              19
  T2                               0                               3
  T2A                              2                               4
  T2A1                             1                               5
  T2A2                             0                               8
  T2B                              3                              10
  T3B                              1                               1
  T4                               0                               1
  TX                               1                               6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V41, continuous

Clustering(53) Variable = DEL PEAK 30(20P12.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(20P12.1) MUTATED    14   7
  DEL PEAK 30(20P12.1) WILD-TYPE 123  25
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            21                            148 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                             7                             25 
$`DEL PEAK 30(20P12.1) MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BK TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A7X5 
       49.48        68.84       177.04        31.40        57.73        13.61 
TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A50E TCGA-EK-A2H0 TCGA-EX-A1H6 TCGA-FU-A3EO 
       12.36         1.35         0.26        45.96         7.92         2.17 
TCGA-FU-A3HY TCGA-FU-A770 TCGA-IR-A3LB TCGA-IR-A3LK TCGA-JW-A5VI TCGA-LP-A4AX 
        0.66         1.12        66.81        26.56        16.64         0.07 
TCGA-MU-A5YI TCGA-RA-A741 TCGA-UC-A7PD 
        0.03         3.88        11.67 

$`DEL PEAK 30(20P12.1) WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        23.67        11.44        18.74        36.56       144.16 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      173.29        82.85         5.46        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       30.21        35.01        53.16        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        2.43        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43         0.82        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       182.93        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       60.69        94.95         9.34         2.73        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18         7.33         8.28         0.76         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-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         0.69        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       12.59         6.64         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-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-A3L1 
        0.07         0.10         0.10         0.03        20.35         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-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-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.35         1.32         1.97        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         4.11       147.39       137.16       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK 
       78.71        81.96        36.36        14.43        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 
       15.58        10.06         5.13         0.10         0.89         0.82 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       13.87         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF 
        4.80         6.25        19.59        93.99 

  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                        177.04                         182.93 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                        12.360                         13.725 
[1] "0.0 - 177.0 (12.4)" "0.0 - 182.9 (13.7)"
[1] "hr=" "2.1"
D53V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 30(20P12.1) MUTATED   13        5
  DEL PEAK 30(20P12.1) WILD-TYPE 84       34
D53V3, multiclass
          clus
vv         DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  T1                                 13                             84
  T2+T3+T4                            5                             34
[1] 2 2
[1] FALSE
D53V4, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED   11  5
  DEL PEAK 30(20P12.1) WILD-TYPE 76 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     11    5
  DEL PEAK 30(20P12.1) WILD-TYPE   76   35
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                           11                             76
  1                            5                             35
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 30(20P12.1) MUTATED   10  0  8
  DEL PEAK 30(20P12.1) WILD-TYPE 62  3 57
D53V5, multiclass
    clus
vv   DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  M0                           10                             62
  M1                            0                              3
  MX                            8                             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(20P12.1) MUTATED               0                               18
  DEL PEAK 30(20P12.1) WILD-TYPE             2                              126
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 30(20P12.1) MUTATED                                               1
  DEL PEAK 30(20P12.1) WILD-TYPE                                             3
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 30(20P12.1) MUTATED                                     4
  DEL PEAK 30(20P12.1) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 30(20P12.1) MUTATED                                           0
  DEL PEAK 30(20P12.1) WILD-TYPE                                         2
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 30(20P12.1) MUTATED                                              0
  DEL PEAK 30(20P12.1) WILD-TYPE                                            4
D53V6, multiclass
                                               clus
vv                                              DEL PEAK 30(20P12.1) MUTATED
  ADENOSQUAMOUS                                                            0
  CERVICAL SQUAMOUS CELL CARCINOMA                                        18
  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                                              DEL PEAK 30(20P12.1) WILD-TYPE
  ADENOSQUAMOUS                                                              2
  CERVICAL SQUAMOUS CELL CARCINOMA                                         126
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              3
  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"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED     2  21
  DEL PEAK 30(20P12.1) WILD-TYPE  25 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      2   21
  DEL PEAK 30(20P12.1) WILD-TYPE   25  128
     clus
vv    DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  NO                             2                             25
  YES                           21                            128
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(20P12.1) MUTATED                                  2     3
  DEL PEAK 30(20P12.1) WILD-TYPE                                5    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(20P12.1) MUTATED                           3
  DEL PEAK 30(20P12.1) WILD-TYPE                        15
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(20P12.1) MUTATED                                           0
  DEL PEAK 30(20P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 30(20P12.1) MUTATED      15
  DEL PEAK 30(20P12.1) WILD-TYPE   115
D53V10, multiclass
                                           clus
vv                                          DEL PEAK 30(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               15
                                           clus
vv                                          DEL PEAK 30(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       5
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D53V11, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED     1  15
  DEL PEAK 30(20P12.1) WILD-TYPE  10 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      1   15
  DEL PEAK 30(20P12.1) WILD-TYPE   10  112
                        clus
vv                       DEL PEAK 30(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       DEL PEAK 30(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            112
[1] 2 2
[1] FALSE
D53V12, continuous
D53V13, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    3  4
  DEL PEAK 30(20P12.1) WILD-TYPE 45 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      3    4
  DEL PEAK 30(20P12.1) WILD-TYPE   45   15
            clus
vv           DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  TUMOR FREE                            3                             45
  WITH TUMOR                            4                             15
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 30(20P12.1) MUTATED         0      2       0            18       3
  DEL PEAK 30(20P12.1) WILD-TYPE       1      8       6           129       9
D53V14, multiclass
               clus
vv              DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  0                              6
  UNITED STATES                           18                            129
  VIETNAM                                  3                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 30(20P12.1) MUTATED    2 12  8  0  1
  DEL PEAK 30(20P12.1) WILD-TYPE 12 71 64  1  4
D53V15, multiclass
    clus
vv   DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  G1                            2                             12
  G2                           12                             71
  G3                            8                             64
  G4                            0                              1
  GX                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V16, continuous
D53V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 30(20P12.1) MUTATED                                             3
  DEL PEAK 30(20P12.1) WILD-TYPE                                          18
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 30(20P12.1) MUTATED                                        3
  DEL PEAK 30(20P12.1) WILD-TYPE                                      5
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 30(20P12.1) MUTATED                                                 0
  DEL PEAK 30(20P12.1) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 30(20P12.1) MUTATED                5                   9
  DEL PEAK 30(20P12.1) WILD-TYPE             31                  74
D53V18, multiclass
                                                 clus
vv                                                DEL PEAK 30(20P12.1) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                     3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                            0
  CURRENT SMOKER                                                             5
  LIFELONG NON-SMOKER                                                        9
                                                 clus
vv                                                DEL PEAK 30(20P12.1) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  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"
D53V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 30(20P12.1) MUTATED             2        4             0        2
  DEL PEAK 30(20P12.1) WILD-TYPE          15       33            11        3
D53V20, multiclass
               clus
vv              DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  COMBINATION                              2                             15
  EXTERNAL                                 4                             33
  EXTERNAL BEAM                            0                             11
  INTERNAL                                 2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V21, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    0  1
  DEL PEAK 30(20P12.1) WILD-TYPE 11  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      0    1
  DEL PEAK 30(20P12.1) WILD-TYPE   11    2
     clus
vv    DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  CGY                            0                             11
  GY                             1                              2
[1] 2 2
[1] FALSE
D53V22, continuous
D53V23, continuous
D53V24, continuous
D53V25, continuous
D53V26, continuous
D53V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 30(20P12.1) MUTATED                                     0
  DEL PEAK 30(20P12.1) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 30(20P12.1) MUTATED                                     1
  DEL PEAK 30(20P12.1) WILD-TYPE                                   5
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 30(20P12.1) MUTATED                         2
  DEL PEAK 30(20P12.1) WILD-TYPE                       7
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 30(20P12.1) MUTATED                         1
  DEL PEAK 30(20P12.1) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 30(20P12.1) MUTATED                         1
  DEL PEAK 30(20P12.1) WILD-TYPE                       4
D53V28, multiclass
                                     clus
vv                                    DEL PEAK 30(20P12.1) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            1
  OTHER LOCATION, SPECIFY                                        2
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        1
                                     clus
vv                                    DEL PEAK 30(20P12.1) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              5
  OTHER LOCATION, SPECIFY                                          7
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 30(20P12.1) MUTATED                                               0
  DEL PEAK 30(20P12.1) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 30(20P12.1) MUTATED                                                1
  DEL PEAK 30(20P12.1) WILD-TYPE                                              9
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 30(20P12.1) MUTATED                                                                                   9
  DEL PEAK 30(20P12.1) WILD-TYPE                                                                                45
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 30(20P12.1) MUTATED                                                                                             10
  DEL PEAK 30(20P12.1) WILD-TYPE                                                                                           67
D53V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 30(20P12.1) 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)                           10
                                                                                              clus
vv                                                                                             DEL PEAK 30(20P12.1) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                             2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                            9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                        45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V30, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    7  7
  DEL PEAK 30(20P12.1) WILD-TYPE 47 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      7    7
  DEL PEAK 30(20P12.1) WILD-TYPE   47   52
         clus
vv        DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  ABSENT                             7                             47
  PRESENT                            7                             52
[1] 2 2
[1] FALSE
D53V31, continuous
D53V32, continuous
D53V33, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    3 10
  DEL PEAK 30(20P12.1) WILD-TYPE 32 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      3   10
  DEL PEAK 30(20P12.1) WILD-TYPE   32   71
                                          clus
vv                                         DEL PEAK 30(20P12.1) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                3
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           10
                                          clus
vv                                         DEL PEAK 30(20P12.1) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             71
[1] 2 2
[1] FALSE
D53V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 30(20P12.1) MUTATED       1                   14                   1
  DEL PEAK 30(20P12.1) WILD-TYPE     2                   99                   4
D53V35, multiclass
                      clus
vv                     DEL PEAK 30(20P12.1) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           14
  SIMPLE HYSTERECTOMY                             1
                      clus
vv                     DEL PEAK 30(20P12.1) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             99
  SIMPLE HYSTERECTOMY                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 30(20P12.1) MUTATED              1           9          3
  DEL PEAK 30(20P12.1) WILD-TYPE            7          31         37
D53V36, multiclass
              clus
vv             DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  CURRENT USER                            1                              7
  FORMER USER                             9                             31
  NEVER USED                              3                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V37, continuous
D53V38, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    9  3
  DEL PEAK 30(20P12.1) WILD-TYPE 64 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      9    3
  DEL PEAK 30(20P12.1) WILD-TYPE   64   11
         clus
vv        DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  ABSENT                             9                             64
  PRESENT                            3                             11
[1] 2 2
[1] FALSE
D53V39, continuous
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 30(20P12.1) MUTATED     0    1   5    5    2  0   0    0    1   3
  DEL PEAK 30(20P12.1) WILD-TYPE   2    0  17   46   19  3   6    6    7  10
                                vv
clus                             T3B T4 TX
  DEL PEAK 30(20P12.1) MUTATED     0  1  0
  DEL PEAK 30(20P12.1) WILD-TYPE   2  0  7
D53V40, multiclass
      clus
vv     DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  T1A                             0                              2
  T1A1                            1                              0
  T1B                             5                             17
  T1B1                            5                             46
  T1B2                            2                             19
  T2                              0                              3
  T2A                             0                              6
  T2A1                            0                              6
  T2A2                            1                              7
  T2B                             3                             10
  T3B                             0                              2
  T4                              1                              0
  TX                              0                              7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V41, continuous

Clustering(54) Variable = DEL PEAK 31(21Q11.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(21Q11.2) MUTATED    23   9
  DEL PEAK 31(21Q11.2) WILD-TYPE 114  23
  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                            32                            137 
  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                             9                             23 
$`DEL PEAK 31(21Q11.2) MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MN 
       57.04        23.67        11.44        35.01         0.46        40.93 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CJ TCGA-C5-A7X3 TCGA-DR-A0ZL TCGA-DS-A0VL 
       73.18        73.45       101.82         9.34        87.75         2.66 
TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A50E TCGA-EA-A556 TCGA-EK-A2GZ 
        1.32         1.35        14.50         0.26        14.89        12.59 
TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-FU-A23L 
        0.53         1.18        23.70         0.03         6.94        23.84 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3LB TCGA-JW-A5VG 
        0.66         1.45        21.67         4.11        66.81        14.43 
TCGA-LP-A4AW TCGA-PN-A8MA 
        0.89         2.96 

$`DEL PEAK 31(21Q11.2) 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-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        2.43         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-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      182.93        25.35       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 
       17.19        85.55        60.69        94.95        13.61         2.73 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76       117.99       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18         7.33         8.28         0.76        12.36         1.74 
TCGA-EA-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-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
        1.81        12.66        12.82         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.99        14.96        13.58        13.48        45.96         6.64 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RM 
        0.59         0.07         4.04         0.03         0.36         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.07         0.10         0.10        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         4.47         6.12         1.22         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.02         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      147.39       137.16       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        36.36        16.64        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
       10.06         5.13         0.10         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
        0.03         5.42        29.72         0.07         4.34         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.45         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        19.59         3.88        11.67        93.99 

  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                        101.82                         182.93 
  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                        12.015                         13.610 
[1] "0.0 - 101.8 (12.0)" "0.0 - 182.9 (13.6)"
[1] "hr=" "2.1"
D54V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 31(21Q11.2) MUTATED   17       10
  DEL PEAK 31(21Q11.2) WILD-TYPE 80       29
D54V3, multiclass
          clus
vv         DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  T1                                 17                             80
  T2+T3+T4                           10                             29
[1] 2 2
[1] FALSE
D54V4, binary
                                cls
clus                              0  1
  DEL PEAK 31(21Q11.2) MUTATED   17  9
  DEL PEAK 31(21Q11.2) WILD-TYPE 70 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(21Q11.2) MUTATED     17    9
  DEL PEAK 31(21Q11.2) WILD-TYPE   70   31
   clus
vv  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  0                           17                             70
  1                            9                             31
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 31(21Q11.2) MUTATED   15  1 11
  DEL PEAK 31(21Q11.2) WILD-TYPE 57  2 54
D54V5, multiclass
    clus
vv   DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  M0                           15                             57
  M1                            1                              2
  MX                           11                             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(21Q11.2) MUTATED               1                               27
  DEL PEAK 31(21Q11.2) WILD-TYPE             1                              117
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 31(21Q11.2) MUTATED                                               0
  DEL PEAK 31(21Q11.2) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 31(21Q11.2) MUTATED                                     4
  DEL PEAK 31(21Q11.2) WILD-TYPE                                  16
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 31(21Q11.2) MUTATED                                           1
  DEL PEAK 31(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 31(21Q11.2) MUTATED                                              0
  DEL PEAK 31(21Q11.2) WILD-TYPE                                            4
D54V6, multiclass
                                               clus
vv                                              DEL PEAK 31(21Q11.2) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        27
  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                                              DEL PEAK 31(21Q11.2) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         117
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(21Q11.2) MUTATED     5  28
  DEL PEAK 31(21Q11.2) WILD-TYPE  22 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(21Q11.2) MUTATED      5   28
  DEL PEAK 31(21Q11.2) WILD-TYPE   22  121
     clus
vv    DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  NO                             5                             22
  YES                           28                            121
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(21Q11.2) MUTATED                                  1     4
  DEL PEAK 31(21Q11.2) WILD-TYPE                                6    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(21Q11.2) MUTATED                           8
  DEL PEAK 31(21Q11.2) WILD-TYPE                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(21Q11.2) MUTATED                                           0
  DEL PEAK 31(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 31(21Q11.2) MUTATED      20
  DEL PEAK 31(21Q11.2) WILD-TYPE   110
D54V10, multiclass
                                           clus
vv                                          DEL PEAK 31(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               20
                                           clus
vv                                          DEL PEAK 31(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D54V11, binary
                                cls
clus                              0  1
  DEL PEAK 31(21Q11.2) MUTATED    1 28
  DEL PEAK 31(21Q11.2) WILD-TYPE 10 99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(21Q11.2) MUTATED      1   28
  DEL PEAK 31(21Q11.2) WILD-TYPE   10   99
                        clus
vv                       DEL PEAK 31(21Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       DEL PEAK 31(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             99
[1] 2 2
[1] FALSE
D54V12, continuous
D54V13, binary
                                cls
clus                              0  1
  DEL PEAK 31(21Q11.2) MUTATED   10  4
  DEL PEAK 31(21Q11.2) WILD-TYPE 38 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(21Q11.2) MUTATED     10    4
  DEL PEAK 31(21Q11.2) WILD-TYPE   38   15
            clus
vv           DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  TUMOR FREE                           10                             38
  WITH TUMOR                            4                             15
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 31(21Q11.2) MUTATED         1      3       0            26       3
  DEL PEAK 31(21Q11.2) WILD-TYPE       0      7       6           121       9
D54V14, multiclass
               clus
vv              DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  NIGERIA                                  1                              0
  RUSSIA                                   3                              7
  UKRAINE                                  0                              6
  UNITED STATES                           26                            121
  VIETNAM                                  3                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 31(21Q11.2) MUTATED    1 12 20  0  0
  DEL PEAK 31(21Q11.2) WILD-TYPE 13 71 52  1  5
D54V15, multiclass
    clus
vv   DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  G1                            1                             13
  G2                           12                             71
  G3                           20                             52
  G4                            0                              1
  GX                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V16, continuous
[1] "Remove cluster labels:"       "DEL PEAK 31(21Q11.2) MUTATED"
clus
  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                             1                             24 
                    TCGA-BI-A0VR                     TCGA-C5-A1BJ 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1BL                     TCGA-C5-A1BQ 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1ME                     TCGA-C5-A1MF 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1MH                     TCGA-C5-A2M2 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A3HD                     TCGA-C5-A7CM 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A7CO                     TCGA-DS-A3LQ 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-EX-A69M                     TCGA-FU-A2QG 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-FU-A3TX                     TCGA-FU-A3WB 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-HM-A4S6 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-IR-A3L7                     TCGA-IR-A3LH 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-MU-A5YI                     TCGA-MU-A8JM 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-Q1-A6DW                     TCGA-RA-A741 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
D54V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 31(21Q11.2) MUTATED                                             0
  DEL PEAK 31(21Q11.2) WILD-TYPE                                          21
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 31(21Q11.2) MUTATED                                        1
  DEL PEAK 31(21Q11.2) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 31(21Q11.2) MUTATED                                                 0
  DEL PEAK 31(21Q11.2) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 31(21Q11.2) MUTATED                9                  14
  DEL PEAK 31(21Q11.2) WILD-TYPE             27                  69
D54V18, multiclass
                                                 clus
vv                                                DEL PEAK 31(21Q11.2) 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                                                             9
  LIFELONG NON-SMOKER                                                       14
                                                 clus
vv                                                DEL PEAK 31(21Q11.2) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              27
  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"
D54V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 31(21Q11.2) MUTATED             1        7             4        0
  DEL PEAK 31(21Q11.2) WILD-TYPE          16       30             7        5
D54V20, multiclass
               clus
vv              DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  COMBINATION                              1                             16
  EXTERNAL                                 7                             30
  EXTERNAL BEAM                            4                              7
  INTERNAL                                 0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V21, binary
                                cls
clus                             0 1
  DEL PEAK 31(21Q11.2) MUTATED   5 0
  DEL PEAK 31(21Q11.2) WILD-TYPE 6 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(21Q11.2) MUTATED      5    0
  DEL PEAK 31(21Q11.2) WILD-TYPE    6    3
     clus
vv    DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  CGY                            5                              6
  GY                             0                              3
[1] 2 2
[1] FALSE
D54V22, continuous
D54V23, continuous
D54V24, continuous
D54V25, continuous
D54V26, continuous
D54V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 31(21Q11.2) MUTATED                                     0
  DEL PEAK 31(21Q11.2) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 31(21Q11.2) MUTATED                                     2
  DEL PEAK 31(21Q11.2) WILD-TYPE                                   4
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 31(21Q11.2) MUTATED                         1
  DEL PEAK 31(21Q11.2) WILD-TYPE                       8
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 31(21Q11.2) MUTATED                         1
  DEL PEAK 31(21Q11.2) WILD-TYPE                       0
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 31(21Q11.2) MUTATED                         0
  DEL PEAK 31(21Q11.2) WILD-TYPE                       5
D54V28, multiclass
                                     clus
vv                                    DEL PEAK 31(21Q11.2) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            2
  OTHER LOCATION, SPECIFY                                        1
  POSITIVE BLADDER MARGIN                                        1
  POSITIVE VAGINAL MARGIN                                        0
                                     clus
vv                                    DEL PEAK 31(21Q11.2) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              4
  OTHER LOCATION, SPECIFY                                          8
  POSITIVE BLADDER MARGIN                                          0
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 31(21Q11.2) MUTATED                                               0
  DEL PEAK 31(21Q11.2) WILD-TYPE                                             2
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 31(21Q11.2) MUTATED                                                1
  DEL PEAK 31(21Q11.2) WILD-TYPE                                              9
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 31(21Q11.2) MUTATED                                                                                   8
  DEL PEAK 31(21Q11.2) WILD-TYPE                                                                                46
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 31(21Q11.2) MUTATED                                                                                             17
  DEL PEAK 31(21Q11.2) WILD-TYPE                                                                                           60
D54V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 31(21Q11.2) 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)                                       8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                           17
                                                                                              clus
vv                                                                                             DEL PEAK 31(21Q11.2) 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)                                        46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V30, binary
                                cls
clus                              0  1
  DEL PEAK 31(21Q11.2) MUTATED   10 13
  DEL PEAK 31(21Q11.2) WILD-TYPE 44 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(21Q11.2) MUTATED     10   13
  DEL PEAK 31(21Q11.2) WILD-TYPE   44   46
         clus
vv        DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  ABSENT                            10                             44
  PRESENT                           13                             46
[1] 2 2
[1] FALSE
D54V31, continuous
D54V32, continuous
D54V33, binary
                                cls
clus                              0  1
  DEL PEAK 31(21Q11.2) MUTATED    6 18
  DEL PEAK 31(21Q11.2) WILD-TYPE 29 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(21Q11.2) MUTATED      6   18
  DEL PEAK 31(21Q11.2) WILD-TYPE   29   63
                                          clus
vv                                         DEL PEAK 31(21Q11.2) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                6
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           18
                                          clus
vv                                         DEL PEAK 31(21Q11.2) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             63
[1] 2 2
[1] FALSE
D54V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 31(21Q11.2) MUTATED       1                   24                   0
  DEL PEAK 31(21Q11.2) WILD-TYPE     2                   89                   5
D54V35, multiclass
                      clus
vv                     DEL PEAK 31(21Q11.2) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           24
  SIMPLE HYSTERECTOMY                             0
                      clus
vv                     DEL PEAK 31(21Q11.2) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             89
  SIMPLE HYSTERECTOMY                               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 31(21Q11.2) MUTATED              2           8          8
  DEL PEAK 31(21Q11.2) WILD-TYPE            6          32         32
D54V36, multiclass
              clus
vv             DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                             8                             32
  NEVER USED                              8                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V37, continuous
D54V38, binary
                                cls
clus                              0  1
  DEL PEAK 31(21Q11.2) MUTATED   13  5
  DEL PEAK 31(21Q11.2) WILD-TYPE 60  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(21Q11.2) MUTATED     13    5
  DEL PEAK 31(21Q11.2) WILD-TYPE   60    9
         clus
vv        DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  ABSENT                            13                             60
  PRESENT                            5                              9
[1] 2 2
[1] FALSE
D54V39, continuous
[1] "Remove cluster labels:"       "DEL PEAK 31(21Q11.2) MUTATED"
clus
  DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE 
                             1                              8 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-JW-A852 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                    TCGA-MU-A51Y                     TCGA-MU-A8JM 
"DEL PEAK 31(21Q11.2) WILD-TYPE" "DEL PEAK 31(21Q11.2) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 31(21Q11.2) MUTATED     1    0   3   11    2  0   4    3    0   1
  DEL PEAK 31(21Q11.2) WILD-TYPE   1    1  19   40   19  3   2    3    8  12
                                vv
clus                             T3B T4 TX
  DEL PEAK 31(21Q11.2) MUTATED     1  1  1
  DEL PEAK 31(21Q11.2) WILD-TYPE   1  0  6
D54V40, multiclass
      clus
vv     DEL PEAK 31(21Q11.2) MUTATED DEL PEAK 31(21Q11.2) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             3                             19
  T1B1                           11                             40
  T1B2                            2                             19
  T2                              0                              3
  T2A                             4                              2
  T2A1                            3                              3
  T2A2                            0                              8
  T2B                             1                             12
  T3B                             1                              1
  T4                              1                              0
  TX                              1                              6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V41, continuous

Clustering(55) Variable = DEL PEAK 32(22Q13.32) MUTATION ANALYSIS
D55V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(22Q13.32) MUTATED    36   9
  DEL PEAK 32(22Q13.32) WILD-TYPE 101  23
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             45                             124 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                              9                              23 
$`DEL PEAK 32(22Q13.32) 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-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD 
       57.73         0.46        40.93        73.18        83.05        52.01 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 
        9.34         2.73       118.65        12.36         1.32         1.35 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG 
       14.50        12.66        14.89        13.58        12.59         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-FU-A23K 
        0.59         1.18         0.10         0.10        20.35         1.22 
TCGA-FU-A3HY TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
        0.66        21.67        14.93       137.16        66.81       117.40 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A852 TCGA-LP-A4AW TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       14.43        16.64         5.13         0.89         3.72         3.45 
TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PD 
        3.39        19.59        11.67 

$`DEL PEAK 32(22Q13.32) 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-A1MP TCGA-C5-A2LS 
       53.16        38.99        35.61         2.43         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       73.45        78.35       100.14        38.43         0.82        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       182.93        25.35       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48         9.67        73.41        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       94.95        13.61        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        0.76         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       14.50         1.35         1.81        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 
       13.91         0.69        14.99        14.96        13.48        45.96 
TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        6.64         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        2.24         0.07         0.10         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         4.47         6.12        23.84         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK 
        1.35         1.32         1.97         1.12        25.41        20.78 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
        4.11       147.39        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AU 
       36.36        19.33        20.48        15.58        10.06         0.10 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        0.07         4.34         2.96         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PF 
        4.80         6.25         3.88        93.99 

  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                         173.29                          182.93 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                         13.580                          13.545 
[1] "0.1 - 173.3 (13.6)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.1"
D55V2, continuous
                                 vv
clus                              T1 T2+T3+T4
  DEL PEAK 32(22Q13.32) MUTATED   25       10
  DEL PEAK 32(22Q13.32) WILD-TYPE 72       29
D55V3, multiclass
          clus
vv         DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  T1                                  25                              72
  T2+T3+T4                            10                              29
[1] 2 2
[1] FALSE
D55V4, binary
                                 cls
clus                               0  1
  DEL PEAK 32(22Q13.32) MUTATED   21 13
  DEL PEAK 32(22Q13.32) WILD-TYPE 66 27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     21   13
  DEL PEAK 32(22Q13.32) WILD-TYPE   66   27
   clus
vv  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  0                            21                              66
  1                            13                              27
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 32(22Q13.32) MUTATED   20  0 17
  DEL PEAK 32(22Q13.32) WILD-TYPE 52  3 48
D55V5, multiclass
    clus
vv   DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  M0                            20                              52
  M1                             0                               3
  MX                            17                              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ADENOSQUAMOUS
  DEL PEAK 32(22Q13.32) MUTATED               0
  DEL PEAK 32(22Q13.32) WILD-TYPE             2
                                 vv
clus                              CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(22Q13.32) MUTATED                                 39
  DEL PEAK 32(22Q13.32) WILD-TYPE                              105
                                 vv
clus                              ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 32(22Q13.32) MUTATED                                               0
  DEL PEAK 32(22Q13.32) WILD-TYPE                                             4
                                 vv
clus                              ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 32(22Q13.32) MUTATED                                     4
  DEL PEAK 32(22Q13.32) WILD-TYPE                                  16
                                 vv
clus                              ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 32(22Q13.32) MUTATED                                           2
  DEL PEAK 32(22Q13.32) WILD-TYPE                                         0
                                 vv
clus                              MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 32(22Q13.32) MUTATED                                              2
  DEL PEAK 32(22Q13.32) WILD-TYPE                                            2
D55V6, multiclass
                                               clus
vv                                              DEL PEAK 32(22Q13.32) MUTATED
  ADENOSQUAMOUS                                                             0
  CERVICAL SQUAMOUS CELL CARCINOMA                                         39
  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                                              DEL PEAK 32(22Q13.32) WILD-TYPE
  ADENOSQUAMOUS                                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                                          105
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                               4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                        16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                                2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    11  36
  DEL PEAK 32(22Q13.32) WILD-TYPE  16 113
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     11   36
  DEL PEAK 32(22Q13.32) WILD-TYPE   16  113
     clus
vv    DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  NO                             11                              16
  YES                            36                             113
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(22Q13.32) MUTATED                                  3     3
  DEL PEAK 32(22Q13.32) WILD-TYPE                                4    12
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(22Q13.32) MUTATED                           4
  DEL PEAK 32(22Q13.32) WILD-TYPE                        14
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 32(22Q13.32) MUTATED                                           1
  DEL PEAK 32(22Q13.32) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 32(22Q13.32) MUTATED      36
  DEL PEAK 32(22Q13.32) WILD-TYPE    94
D55V10, multiclass
                                           clus
vv                                          DEL PEAK 32(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 3
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                36
                                           clus
vv                                          DEL PEAK 32(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  12
  BLACK OR AFRICAN AMERICAN                                              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                  94
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, binary
                                 cls
clus                               0  1
  DEL PEAK 32(22Q13.32) MUTATED    4 33
  DEL PEAK 32(22Q13.32) WILD-TYPE  7 94
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED      4   33
  DEL PEAK 32(22Q13.32) WILD-TYPE    7   94
                        clus
vv                       DEL PEAK 32(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            33
                        clus
vv                       DEL PEAK 32(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                              94
[1] 2 2
[1] FALSE
D55V12, continuous
D55V13, binary
                                 cls
clus                               0  1
  DEL PEAK 32(22Q13.32) MUTATED   18  4
  DEL PEAK 32(22Q13.32) WILD-TYPE 30 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     18    4
  DEL PEAK 32(22Q13.32) WILD-TYPE   30   15
            clus
vv           DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  TUMOR FREE                            18                              30
  WITH TUMOR                             4                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 32(22Q13.32) MUTATED         0      4       1            39       3
  DEL PEAK 32(22Q13.32) WILD-TYPE       1      6       5           108       9
D55V14, multiclass
               clus
vv              DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  NIGERIA                                   0                               1
  RUSSIA                                    4                               6
  UKRAINE                                   1                               5
  UNITED STATES                            39                             108
  VIETNAM                                   3                               9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              G1 G2 G3 G4 GX
  DEL PEAK 32(22Q13.32) MUTATED    3 20 23  0  1
  DEL PEAK 32(22Q13.32) WILD-TYPE 11 63 49  1  4
D55V15, multiclass
    clus
vv   DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  G1                             3                              11
  G2                            20                              63
  G3                            23                              49
  G4                             0                               1
  GX                             1                               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V16, continuous
D55V17, continuous
                                 vv
clus                              CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 32(22Q13.32) MUTATED                                             3
  DEL PEAK 32(22Q13.32) WILD-TYPE                                          18
                                 vv
clus                              CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 32(22Q13.32) MUTATED                                        2
  DEL PEAK 32(22Q13.32) WILD-TYPE                                      6
                                 vv
clus                              CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 32(22Q13.32) MUTATED                                                 0
  DEL PEAK 32(22Q13.32) WILD-TYPE                                               1
                                 vv
clus                              CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 32(22Q13.32) MUTATED               11                  22
  DEL PEAK 32(22Q13.32) WILD-TYPE             25                  61
D55V18, multiclass
                                                 clus
vv                                                DEL PEAK 32(22Q13.32) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             0
  CURRENT SMOKER                                                             11
  LIFELONG NON-SMOKER                                                        22
                                                 clus
vv                                                DEL PEAK 32(22Q13.32) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                  18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                        6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                               1
  CURRENT SMOKER                                                               25
  LIFELONG NON-SMOKER                                                          61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V19, continuous
                                 vv
clus                              COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 32(22Q13.32) MUTATED             6       11             4        1
  DEL PEAK 32(22Q13.32) WILD-TYPE          11       26             7        4
D55V20, multiclass
               clus
vv              DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  COMBINATION                               6                              11
  EXTERNAL                                 11                              26
  EXTERNAL BEAM                             4                               7
  INTERNAL                                  1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V21, binary
                                 cls
clus                              0 1
  DEL PEAK 32(22Q13.32) MUTATED   3 1
  DEL PEAK 32(22Q13.32) WILD-TYPE 8 2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED      3    1
  DEL PEAK 32(22Q13.32) WILD-TYPE    8    2
     clus
vv    DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  CGY                             3                               8
  GY                              1                               2
[1] 2 2
[1] FALSE
D55V22, continuous
D55V23, continuous
D55V24, continuous
D55V25, continuous
D55V26, continuous
D55V27, continuous
                                 vv
clus                              MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 32(22Q13.32) MUTATED                                     0
  DEL PEAK 32(22Q13.32) WILD-TYPE                                   2
                                 vv
clus                              MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 32(22Q13.32) MUTATED                                     2
  DEL PEAK 32(22Q13.32) WILD-TYPE                                   4
                                 vv
clus                              OTHER LOCATION, SPECIFY
  DEL PEAK 32(22Q13.32) MUTATED                         4
  DEL PEAK 32(22Q13.32) WILD-TYPE                       5
                                 vv
clus                              POSITIVE BLADDER MARGIN
  DEL PEAK 32(22Q13.32) MUTATED                         0
  DEL PEAK 32(22Q13.32) WILD-TYPE                       1
                                 vv
clus                              POSITIVE VAGINAL MARGIN
  DEL PEAK 32(22Q13.32) MUTATED                         1
  DEL PEAK 32(22Q13.32) WILD-TYPE                       4
D55V28, multiclass
                                     clus
vv                                    DEL PEAK 32(22Q13.32) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                         4
  POSITIVE BLADDER MARGIN                                         0
  POSITIVE VAGINAL MARGIN                                         1
                                     clus
vv                                    DEL PEAK 32(22Q13.32) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                               2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                               4
  OTHER LOCATION, SPECIFY                                           5
  POSITIVE BLADDER MARGIN                                           1
  POSITIVE VAGINAL MARGIN                                           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)
  DEL PEAK 32(22Q13.32) MUTATED                                               1
  DEL PEAK 32(22Q13.32) WILD-TYPE                                             1
                                 vv
clus                              PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 32(22Q13.32) MUTATED                                                3
  DEL PEAK 32(22Q13.32) WILD-TYPE                                              7
                                 vv
clus                              POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 32(22Q13.32) MUTATED                                                                                  15
  DEL PEAK 32(22Q13.32) WILD-TYPE                                                                                39
                                 vv
clus                              PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 32(22Q13.32) MUTATED                                                                                             20
  DEL PEAK 32(22Q13.32) WILD-TYPE                                                                                           57
D55V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 32(22Q13.32) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            20
                                                                                              clus
vv                                                                                             DEL PEAK 32(22Q13.32) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                             7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                         39
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                              57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V30, binary
                                 cls
clus                               0  1
  DEL PEAK 32(22Q13.32) MUTATED   10 22
  DEL PEAK 32(22Q13.32) WILD-TYPE 44 37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     10   22
  DEL PEAK 32(22Q13.32) WILD-TYPE   44   37
         clus
vv        DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  ABSENT                             10                              44
  PRESENT                            22                              37
[1] 2 2
[1] FALSE
D55V31, continuous
D55V32, continuous
D55V33, binary
                                 cls
clus                               0  1
  DEL PEAK 32(22Q13.32) MUTATED    9 23
  DEL PEAK 32(22Q13.32) WILD-TYPE 26 58
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED      9   23
  DEL PEAK 32(22Q13.32) WILD-TYPE   26   58
                                          clus
vv                                         DEL PEAK 32(22Q13.32) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 9
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            23
                                          clus
vv                                         DEL PEAK 32(22Q13.32) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                  26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                              58
[1] 2 2
[1] FALSE
D55V34, continuous
                                 vv
clus                              OTHER RADICAL HYSTERECTOMY
  DEL PEAK 32(22Q13.32) MUTATED       1                   30
  DEL PEAK 32(22Q13.32) WILD-TYPE     2                   83
                                 vv
clus                              SIMPLE HYSTERECTOMY
  DEL PEAK 32(22Q13.32) MUTATED                     1
  DEL PEAK 32(22Q13.32) WILD-TYPE                   4
D55V35, multiclass
                      clus
vv                     DEL PEAK 32(22Q13.32) MUTATED
  OTHER                                            1
  RADICAL HYSTERECTOMY                            30
  SIMPLE HYSTERECTOMY                              1
                      clus
vv                     DEL PEAK 32(22Q13.32) WILD-TYPE
  OTHER                                              2
  RADICAL HYSTERECTOMY                              83
  SIMPLE HYSTERECTOMY                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CURRENT USER FORMER USER NEVER USED
  DEL PEAK 32(22Q13.32) MUTATED              4          13         12
  DEL PEAK 32(22Q13.32) WILD-TYPE            4          27         28
D55V36, multiclass
              clus
vv             DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  CURRENT USER                             4                               4
  FORMER USER                             13                              27
  NEVER USED                              12                              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V37, continuous
D55V38, binary
                                 cls
clus                               0  1
  DEL PEAK 32(22Q13.32) MUTATED   22  2
  DEL PEAK 32(22Q13.32) WILD-TYPE 51 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     22    2
  DEL PEAK 32(22Q13.32) WILD-TYPE   51   12
         clus
vv        DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  ABSENT                             22                              51
  PRESENT                             2                              12
[1] 2 2
[1] FALSE
D55V39, continuous
                                 vv
clus                              T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 32(22Q13.32) MUTATED     1    0   6   14    4  1   3    1    1   4
  DEL PEAK 32(22Q13.32) WILD-TYPE   1    1  16   37   17  2   3    5    7   9
                                 vv
clus                              T3B T4 TX
  DEL PEAK 32(22Q13.32) MUTATED     0  0  3
  DEL PEAK 32(22Q13.32) WILD-TYPE   2  1  4
D55V40, multiclass
      clus
vv     DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  T1A                              1                               1
  T1A1                             0                               1
  T1B                              6                              16
  T1B1                            14                              37
  T1B2                             4                              17
  T2                               1                               2
  T2A                              3                               3
  T2A1                             1                               5
  T2A2                             1                               7
  T2B                              4                               9
  T3B                              0                               2
  T4                               0                               1
  TX                               3                               4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V41, continuous

Clustering(56) Variable = DEL PEAK 33(XP11.3) MUTATION ANALYSIS
D56V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 33(XP11.3) MUTATED    34   6
  DEL PEAK 33(XP11.3) WILD-TYPE 103  26
  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE 
                           40                           129 
  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE 
                            6                            26 
$`DEL PEAK 33(XP11.3) MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M7 
       57.04        23.67        11.44       177.04         5.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7UH 
       30.21        53.16        40.93        73.45        52.01        60.69 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3QE 
      118.65        22.98        16.18        12.36         1.32         1.18 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2PG 
        1.81        12.66        14.89        14.96        45.96         0.53 
TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A2QG 
        0.07         0.36         0.10         0.10        20.35         0.92 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LK 
        0.66         1.45         1.97       137.16        66.81        26.56 
TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MY-A5BF TCGA-Q1-A6DT 
        0.89         0.82         4.34         3.39 

$`DEL PEAK 33(XP11.3) WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL 
       49.48        68.84        18.74        36.56       144.16       173.29 
TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME 
       82.85        19.86        67.46        31.40        35.01        57.73 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         0.46         2.43         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-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-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       182.93        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       94.95         9.34        13.61         2.73        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI 
       36.76         2.66       117.99        16.83         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 
        0.76         1.74         0.82         0.62        13.05        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
        1.35         1.35        14.50        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       13.91         0.69        14.99        13.58        13.48        12.59 
TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL 
        6.64         0.59         4.04         0.03         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        2.24         0.10         0.07         0.03         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       14.70         4.47         6.12         1.22        23.84         2.17 
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-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
        4.11       147.39       117.40        96.95        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        14.43        16.64        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MU-A51Y TCGA-MU-A5YI 
       10.06         5.13         0.10         0.07        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         0.07         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        5.85         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE 
                       177.04                        182.93 
  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE 
                       13.775                        13.580 
[1] "0.1 - 177.0 (13.8)" "0.0 - 182.9 (13.6)"
[1] "hr=" "1.4"
D56V2, continuous
                               vv
clus                            T1 T2+T3+T4
  DEL PEAK 33(XP11.3) MUTATED   27        6
  DEL PEAK 33(XP11.3) WILD-TYPE 70       33
D56V3, multiclass
          clus
vv         DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  T1                                27                            70
  T2+T3+T4                           6                            33
[1] 2 2
[1] FALSE
D56V4, binary
                               cls
clus                             0  1
  DEL PEAK 33(XP11.3) MUTATED   24  8
  DEL PEAK 33(XP11.3) WILD-TYPE 63 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP11.3) MUTATED     24    8
  DEL PEAK 33(XP11.3) WILD-TYPE   63   32
   clus
vv  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  0                          24                            63
  1                           8                            32
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 33(XP11.3) MUTATED   16  0 16
  DEL PEAK 33(XP11.3) WILD-TYPE 56  3 49
D56V5, multiclass
    clus
vv   DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  M0                          16                            56
  M1                           0                             3
  MX                          16                            49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(XP11.3) MUTATED               1                               38
  DEL PEAK 33(XP11.3) WILD-TYPE             1                              106
                               vv
clus                            ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 33(XP11.3) MUTATED                                               0
  DEL PEAK 33(XP11.3) WILD-TYPE                                             4
                               vv
clus                            ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 33(XP11.3) MUTATED                                     2
  DEL PEAK 33(XP11.3) WILD-TYPE                                  18
                               vv
clus                            ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 33(XP11.3) MUTATED                                           2
  DEL PEAK 33(XP11.3) WILD-TYPE                                         0
                               vv
clus                            MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 33(XP11.3) MUTATED                                              0
  DEL PEAK 33(XP11.3) WILD-TYPE                                            4
D56V6, multiclass
                                               clus
vv                                              DEL PEAK 33(XP11.3) MUTATED
  ADENOSQUAMOUS                                                           1
  CERVICAL SQUAMOUS CELL CARCINOMA                                       38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                           0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                     2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                               2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                            0
                                               clus
vv                                              DEL PEAK 33(XP11.3) WILD-TYPE
  ADENOSQUAMOUS                                                             1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        106
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                             4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                 0
  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"
D56V7, binary
                               cls
clus                              0   1
  DEL PEAK 33(XP11.3) MUTATED     8  35
  DEL PEAK 33(XP11.3) WILD-TYPE  19 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP11.3) MUTATED      8   35
  DEL PEAK 33(XP11.3) WILD-TYPE   19  114
     clus
vv    DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  NO                            8                            19
  YES                          35                           114
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(XP11.3) MUTATED                                  0     3
  DEL PEAK 33(XP11.3) WILD-TYPE                                7    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(XP11.3) MUTATED                           5
  DEL PEAK 33(XP11.3) WILD-TYPE                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 33(XP11.3) MUTATED                                           1    32
  DEL PEAK 33(XP11.3) WILD-TYPE                                         0    98
D56V10, multiclass
                                           clus
vv                                          DEL PEAK 33(XP11.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              32
                                           clus
vv                                          DEL PEAK 33(XP11.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      7
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                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"
D56V11, binary
                               cls
clus                             0  1
  DEL PEAK 33(XP11.3) MUTATED    1 34
  DEL PEAK 33(XP11.3) WILD-TYPE 10 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP11.3) MUTATED      1   34
  DEL PEAK 33(XP11.3) WILD-TYPE   10   93
                        clus
vv                       DEL PEAK 33(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          34
                        clus
vv                       DEL PEAK 33(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                            93
[1] 2 2
[1] FALSE
D56V12, continuous
D56V13, binary
                               cls
clus                             0  1
  DEL PEAK 33(XP11.3) MUTATED   14  5
  DEL PEAK 33(XP11.3) WILD-TYPE 34 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP11.3) MUTATED     14    5
  DEL PEAK 33(XP11.3) WILD-TYPE   34   14
            clus
vv           DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  TUMOR FREE                          14                            34
  WITH TUMOR                           5                            14
[1] 2 2
[1] FALSE
                               vv
clus                            NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 33(XP11.3) MUTATED         0      4       2            34       3
  DEL PEAK 33(XP11.3) WILD-TYPE       1      6       4           113       9
D56V14, multiclass
               clus
vv              DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  NIGERIA                                 0                             1
  RUSSIA                                  4                             6
  UKRAINE                                 2                             4
  UNITED STATES                          34                           113
  VIETNAM                                 3                             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            G1 G2 G3 G4 GX
  DEL PEAK 33(XP11.3) MUTATED    2 17 22  0  1
  DEL PEAK 33(XP11.3) WILD-TYPE 12 66 50  1  4
D56V15, multiclass
    clus
vv   DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  G1                           2                            12
  G2                          17                            66
  G3                          22                            50
  G4                           0                             1
  GX                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V16, continuous
D56V17, continuous
                               vv
clus                            CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 33(XP11.3) MUTATED                                             3
  DEL PEAK 33(XP11.3) WILD-TYPE                                          18
                               vv
clus                            CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 33(XP11.3) MUTATED                                        2
  DEL PEAK 33(XP11.3) WILD-TYPE                                      6
                               vv
clus                            CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 33(XP11.3) MUTATED                                                 0
  DEL PEAK 33(XP11.3) WILD-TYPE                                               1
                               vv
clus                            CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 33(XP11.3) MUTATED               12                  17
  DEL PEAK 33(XP11.3) WILD-TYPE             24                  66
D56V18, multiclass
                                                 clus
vv                                                DEL PEAK 33(XP11.3) MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                               3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                    2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                           0
  CURRENT SMOKER                                                           12
  LIFELONG NON-SMOKER                                                      17
                                                 clus
vv                                                DEL PEAK 33(XP11.3) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                      6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                             1
  CURRENT SMOKER                                                             24
  LIFELONG NON-SMOKER                                                        66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V19, continuous
                               vv
clus                            COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 33(XP11.3) MUTATED             3        4             4        1
  DEL PEAK 33(XP11.3) WILD-TYPE          14       33             7        4
D56V20, multiclass
               clus
vv              DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  COMBINATION                             3                            14
  EXTERNAL                                4                            33
  EXTERNAL BEAM                           4                             7
  INTERNAL                                1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V21, binary
                               cls
clus                            0 1
  DEL PEAK 33(XP11.3) MUTATED   2 0
  DEL PEAK 33(XP11.3) WILD-TYPE 9 3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP11.3) MUTATED      2    0
  DEL PEAK 33(XP11.3) WILD-TYPE    9    3
     clus
vv    DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  CGY                           2                             9
  GY                            0                             3
[1] 2 2
[1] FALSE
D56V22, continuous
D56V23, continuous
D56V24, continuous
D56V25, continuous
D56V26, continuous
D56V27, continuous
                               vv
clus                            MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 33(XP11.3) MUTATED                                     0
  DEL PEAK 33(XP11.3) WILD-TYPE                                   2
                               vv
clus                            MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 33(XP11.3) MUTATED                                     4
  DEL PEAK 33(XP11.3) WILD-TYPE                                   2
                               vv
clus                            OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  DEL PEAK 33(XP11.3) MUTATED                         2                       0
  DEL PEAK 33(XP11.3) WILD-TYPE                       7                       1
                               vv
clus                            POSITIVE VAGINAL MARGIN
  DEL PEAK 33(XP11.3) MUTATED                         0
  DEL PEAK 33(XP11.3) WILD-TYPE                       5
D56V28, multiclass
                                     clus
vv                                    DEL PEAK 33(XP11.3) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                           0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                           4
  OTHER LOCATION, SPECIFY                                       2
  POSITIVE BLADDER MARGIN                                       0
  POSITIVE VAGINAL MARGIN                                       0
                                     clus
vv                                    DEL PEAK 33(XP11.3) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                             2
  OTHER LOCATION, SPECIFY                                         7
  POSITIVE BLADDER MARGIN                                         1
  POSITIVE VAGINAL MARGIN                                         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)
  DEL PEAK 33(XP11.3) MUTATED                                               1
  DEL PEAK 33(XP11.3) WILD-TYPE                                             1
                               vv
clus                            PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 33(XP11.3) MUTATED                                                3
  DEL PEAK 33(XP11.3) WILD-TYPE                                              7
                               vv
clus                            POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 33(XP11.3) MUTATED                                                                                  11
  DEL PEAK 33(XP11.3) WILD-TYPE                                                                                43
                               vv
clus                            PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 33(XP11.3) MUTATED                                                                                             21
  DEL PEAK 33(XP11.3) WILD-TYPE                                                                                           56
D56V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 33(XP11.3) 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)                          21
                                                                                              clus
vv                                                                                             DEL PEAK 33(XP11.3) WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                            1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                           7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                                       43
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                            56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V30, binary
                               cls
clus                             0  1
  DEL PEAK 33(XP11.3) MUTATED   15 15
  DEL PEAK 33(XP11.3) WILD-TYPE 39 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP11.3) MUTATED     15   15
  DEL PEAK 33(XP11.3) WILD-TYPE   39   44
         clus
vv        DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  ABSENT                           15                            39
  PRESENT                          15                            44
[1] 2 2
[1] FALSE
D56V31, continuous
D56V32, continuous
D56V33, binary
                               cls
clus                             0  1
  DEL PEAK 33(XP11.3) MUTATED   12 19
  DEL PEAK 33(XP11.3) WILD-TYPE 23 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP11.3) MUTATED     12   19
  DEL PEAK 33(XP11.3) WILD-TYPE   23   62
                                          clus
vv                                         DEL PEAK 33(XP11.3) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                              12
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                          19
                                          clus
vv                                         DEL PEAK 33(XP11.3) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                            62
[1] 2 2
[1] FALSE
D56V34, continuous
                               vv
clus                            OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 33(XP11.3) MUTATED       2                   29                   1
  DEL PEAK 33(XP11.3) WILD-TYPE     1                   84                   4
D56V35, multiclass
                      clus
vv                     DEL PEAK 33(XP11.3) MUTATED
  OTHER                                          2
  RADICAL HYSTERECTOMY                          29
  SIMPLE HYSTERECTOMY                            1
                      clus
vv                     DEL PEAK 33(XP11.3) WILD-TYPE
  OTHER                                            1
  RADICAL HYSTERECTOMY                            84
  SIMPLE HYSTERECTOMY                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CURRENT USER FORMER USER NEVER USED
  DEL PEAK 33(XP11.3) MUTATED              1           9         16
  DEL PEAK 33(XP11.3) WILD-TYPE            7          31         24
D56V36, multiclass
              clus
vv             DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  CURRENT USER                           1                             7
  FORMER USER                            9                            31
  NEVER USED                            16                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V37, continuous
D56V38, binary
                               cls
clus                             0  1
  DEL PEAK 33(XP11.3) MUTATED   21  1
  DEL PEAK 33(XP11.3) WILD-TYPE 52 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP11.3) MUTATED     21    1
  DEL PEAK 33(XP11.3) WILD-TYPE   52   13
         clus
vv        DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  ABSENT                           21                            52
  PRESENT                           1                            13
[1] 2 2
[1] FALSE
D56V39, continuous
[1] "Remove cluster labels:"      "DEL PEAK 33(XP11.3) MUTATED"
clus
  DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE 
                            2                             7 
                   TCGA-C5-A1MH                    TCGA-C5-A1MP 
"DEL PEAK 33(XP11.3) WILD-TYPE" "DEL PEAK 33(XP11.3) WILD-TYPE" 
                   TCGA-EK-A2RO                    TCGA-HM-A3JK 
"DEL PEAK 33(XP11.3) WILD-TYPE" "DEL PEAK 33(XP11.3) WILD-TYPE" 
                   TCGA-JW-A852                    TCGA-MU-A51Y 
"DEL PEAK 33(XP11.3) WILD-TYPE" "DEL PEAK 33(XP11.3) WILD-TYPE" 
                   TCGA-MU-A8JM 
"DEL PEAK 33(XP11.3) WILD-TYPE" 
                               vv
clus                            T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B
  DEL PEAK 33(XP11.3) MUTATED     2    0   7   12    6  0   1    0    3   1   1
  DEL PEAK 33(XP11.3) WILD-TYPE   0    1  15   39   15  3   5    6    5  12   1
                               vv
clus                            T4 TX
  DEL PEAK 33(XP11.3) MUTATED    0  1
  DEL PEAK 33(XP11.3) WILD-TYPE  1  6
D56V40, multiclass
      clus
vv     DEL PEAK 33(XP11.3) MUTATED DEL PEAK 33(XP11.3) WILD-TYPE
  T1A                            2                             0
  T1A1                           0                             1
  T1B                            7                            15
  T1B1                          12                            39
  T1B2                           6                            15
  T2                             0                             3
  T2A                            1                             5
  T2A1                           0                             6
  T2A2                           3                             5
  T2B                            1                            12
  T3B                            1                             1
  T4                             0                             1
  TX                             1                             6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V41, continuous

Clustering(57) Variable = DEL PEAK 34(XQ21.33) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(XQ21.33) MUTATED    22  11
  DEL PEAK 34(XQ21.33) WILD-TYPE 115  21
  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE 
                            33                            136 
  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE 
                            11                             21 
$`DEL PEAK 34(XQ21.33) MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1MK 
       23.67        11.44        19.86        67.46        30.21         2.43 
TCGA-C5-A1MN TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CJ TCGA-C5-A7CO TCGA-C5-A7X5 
       40.93        83.05        52.01       101.82        73.41        13.61 
TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A44S TCGA-EA-A556 
       36.76       118.65        16.18        12.36        12.66        14.89 
TCGA-EA-A5ZE TCGA-EK-A2IP TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
       14.99         6.64         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-LP-A5U3 TCGA-MY-A5BF 
        5.13         0.82         4.34 

$`DEL PEAK 34(XQ21.33) 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-A1M6 TCGA-C5-A1M7 
      177.04       173.29        82.85         5.46        31.40        46.32 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       35.01        57.73        53.16        38.99        35.61         0.46 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ 
        3.58        44.22        73.18        73.45        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43         0.82        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
       25.35       134.33        15.48         9.67        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       60.69        94.95         9.34         2.73        87.75        58.88 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI 
        2.66       117.99        22.98        16.83         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        0.76         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        1.18        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF 
       12.82         0.26         1.48        13.91         0.69        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 
       13.58        13.48        12.59        45.96         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 
        2.24         0.10         0.07         0.03         6.94        14.70 
TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI 
        4.47         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-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       81.96        36.36        14.43        16.64        19.33        20.48 
TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MU-A51Y TCGA-MU-A5YI 
       10.06         0.10         0.89         0.07        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         0.07         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        5.85         3.39         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE 
                        118.65                         182.93 
  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE 
                        14.890                         13.265 
[1] "0.1 - 118.7 (14.9)" "0.0 - 182.9 (13.3)"
[1] "hr=" "2.3"
D57V2, continuous
                                vv
clus                             T1 T2+T3+T4
  DEL PEAK 34(XQ21.33) MUTATED   22        6
  DEL PEAK 34(XQ21.33) WILD-TYPE 75       33
D57V3, multiclass
          clus
vv         DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  T1                                 22                             75
  T2+T3+T4                            6                             33
[1] 2 2
[1] FALSE
D57V4, binary
                                cls
clus                              0  1
  DEL PEAK 34(XQ21.33) MUTATED   18  9
  DEL PEAK 34(XQ21.33) WILD-TYPE 69 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(XQ21.33) MUTATED     18    9
  DEL PEAK 34(XQ21.33) WILD-TYPE   69   31
   clus
vv  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  0                           18                             69
  1                            9                             31
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 34(XQ21.33) MUTATED   11  0 15
  DEL PEAK 34(XQ21.33) WILD-TYPE 61  3 50
D57V5, multiclass
    clus
vv   DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  M0                           11                             61
  M1                            0                              3
  MX                           15                             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(XQ21.33) MUTATED               1                               32
  DEL PEAK 34(XQ21.33) WILD-TYPE             1                              112
                                vv
clus                             ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  DEL PEAK 34(XQ21.33) MUTATED                                               0
  DEL PEAK 34(XQ21.33) WILD-TYPE                                             4
                                vv
clus                             ENDOCERVICAL TYPE OF ADENOCARCINOMA
  DEL PEAK 34(XQ21.33) MUTATED                                     2
  DEL PEAK 34(XQ21.33) WILD-TYPE                                  18
                                vv
clus                             ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  DEL PEAK 34(XQ21.33) MUTATED                                           1
  DEL PEAK 34(XQ21.33) WILD-TYPE                                         1
                                vv
clus                             MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  DEL PEAK 34(XQ21.33) MUTATED                                              0
  DEL PEAK 34(XQ21.33) WILD-TYPE                                            4
D57V6, multiclass
                                               clus
vv                                              DEL PEAK 34(XQ21.33) MUTATED
  ADENOSQUAMOUS                                                            1
  CERVICAL SQUAMOUS CELL CARCINOMA                                        32
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                            0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                      2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                             0
                                               clus
vv                                              DEL PEAK 34(XQ21.33) WILD-TYPE
  ADENOSQUAMOUS                                                              1
  CERVICAL SQUAMOUS CELL CARCINOMA                                         112
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                              4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                                       18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                                  1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(XQ21.33) MUTATED     7  29
  DEL PEAK 34(XQ21.33) WILD-TYPE  20 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(XQ21.33) MUTATED      7   29
  DEL PEAK 34(XQ21.33) WILD-TYPE   20  120
     clus
vv    DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  NO                             7                             20
  YES                           29                            120
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(XQ21.33) MUTATED                                  1     2
  DEL PEAK 34(XQ21.33) WILD-TYPE                                6    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(XQ21.33) MUTATED                           3
  DEL PEAK 34(XQ21.33) WILD-TYPE                        15
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 34(XQ21.33) MUTATED                                           1
  DEL PEAK 34(XQ21.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 34(XQ21.33) MUTATED      28
  DEL PEAK 34(XQ21.33) WILD-TYPE   102
D57V10, multiclass
                                           clus
vv                                          DEL PEAK 34(XQ21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               28
                                           clus
vv                                          DEL PEAK 34(XQ21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       6
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D57V11, binary
                                cls
clus                               0   1
  DEL PEAK 34(XQ21.33) MUTATED     3  26
  DEL PEAK 34(XQ21.33) WILD-TYPE   8 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(XQ21.33) MUTATED      3   26
  DEL PEAK 34(XQ21.33) WILD-TYPE    8  101
                        clus
vv                       DEL PEAK 34(XQ21.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       DEL PEAK 34(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            101
[1] 2 2
[1] FALSE
D57V12, continuous
D57V13, binary
                                cls
clus                              0  1
  DEL PEAK 34(XQ21.33) MUTATED   13  5
  DEL PEAK 34(XQ21.33) WILD-TYPE 35 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(XQ21.33) MUTATED     13    5
  DEL PEAK 34(XQ21.33) WILD-TYPE   35   14
            clus
vv           DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  TUMOR FREE                           13                             35
  WITH TUMOR                            5                             14
[1] 2 2
[1] FALSE
                                vv
clus                             NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  DEL PEAK 34(XQ21.33) MUTATED         0      2       1            31       2
  DEL PEAK 34(XQ21.33) WILD-TYPE       1      8       5           116      10
D57V14, multiclass
               clus
vv              DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  NIGERIA                                  0                              1
  RUSSIA                                   2                              8
  UKRAINE                                  1                              5
  UNITED STATES                           31                            116
  VIETNAM                                  2                             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             G1 G2 G3 G4 GX
  DEL PEAK 34(XQ21.33) MUTATED    3 14 18  0  0
  DEL PEAK 34(XQ21.33) WILD-TYPE 11 69 54  1  5
D57V15, multiclass
    clus
vv   DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  G1                            3                             11
  G2                           14                             69
  G3                           18                             54
  G4                            0                              1
  GX                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V16, continuous
D57V17, continuous
                                vv
clus                             CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  DEL PEAK 34(XQ21.33) MUTATED                                             5
  DEL PEAK 34(XQ21.33) WILD-TYPE                                          16
                                vv
clus                             CURRENT REFORMED SMOKER FOR > 15 YEARS
  DEL PEAK 34(XQ21.33) MUTATED                                        1
  DEL PEAK 34(XQ21.33) WILD-TYPE                                      7
                                vv
clus                             CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  DEL PEAK 34(XQ21.33) MUTATED                                                 0
  DEL PEAK 34(XQ21.33) WILD-TYPE                                               1
                                vv
clus                             CURRENT SMOKER LIFELONG NON-SMOKER
  DEL PEAK 34(XQ21.33) MUTATED                8                  14
  DEL PEAK 34(XQ21.33) WILD-TYPE             28                  69
D57V18, multiclass
                                                 clus
vv                                                DEL PEAK 34(XQ21.33) 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                                                             8
  LIFELONG NON-SMOKER                                                       14
                                                 clus
vv                                                DEL PEAK 34(XQ21.33) WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                                 16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                                       7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                              1
  CURRENT SMOKER                                                              28
  LIFELONG NON-SMOKER                                                         69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V19, continuous
                                vv
clus                             COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  DEL PEAK 34(XQ21.33) MUTATED             4        4             4        1
  DEL PEAK 34(XQ21.33) WILD-TYPE          13       33             7        4
D57V20, multiclass
               clus
vv              DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  COMBINATION                              4                             13
  EXTERNAL                                 4                             33
  EXTERNAL BEAM                            4                              7
  INTERNAL                                 1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V21, binary
                                cls
clus                             0 1
  DEL PEAK 34(XQ21.33) MUTATED   3 0
  DEL PEAK 34(XQ21.33) WILD-TYPE 8 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(XQ21.33) MUTATED      3    0
  DEL PEAK 34(XQ21.33) WILD-TYPE    8    3
     clus
vv    DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  CGY                            3                              8
  GY                             0                              3
[1] 2 2
[1] FALSE
D57V22, continuous
D57V23, continuous
D57V24, continuous
D57V25, continuous
D57V26, continuous
D57V27, continuous
                                vv
clus                             MACROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 34(XQ21.33) MUTATED                                     0
  DEL PEAK 34(XQ21.33) WILD-TYPE                                   2
                                vv
clus                             MICROSCOPIC PARAMETRIAL INVOLVEMENT
  DEL PEAK 34(XQ21.33) MUTATED                                     4
  DEL PEAK 34(XQ21.33) WILD-TYPE                                   2
                                vv
clus                             OTHER LOCATION, SPECIFY
  DEL PEAK 34(XQ21.33) MUTATED                         1
  DEL PEAK 34(XQ21.33) WILD-TYPE                       8
                                vv
clus                             POSITIVE BLADDER MARGIN
  DEL PEAK 34(XQ21.33) MUTATED                         0
  DEL PEAK 34(XQ21.33) WILD-TYPE                       1
                                vv
clus                             POSITIVE VAGINAL MARGIN
  DEL PEAK 34(XQ21.33) MUTATED                         2
  DEL PEAK 34(XQ21.33) WILD-TYPE                       3
D57V28, multiclass
                                     clus
vv                                    DEL PEAK 34(XQ21.33) MUTATED
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                            0
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                            4
  OTHER LOCATION, SPECIFY                                        1
  POSITIVE BLADDER MARGIN                                        0
  POSITIVE VAGINAL MARGIN                                        2
                                     clus
vv                                    DEL PEAK 34(XQ21.33) WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                              2
  OTHER LOCATION, SPECIFY                                          8
  POSITIVE BLADDER MARGIN                                          1
  POSITIVE VAGINAL MARGIN                                          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)
  DEL PEAK 34(XQ21.33) MUTATED                                               2
  DEL PEAK 34(XQ21.33) WILD-TYPE                                             0
                                vv
clus                             PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  DEL PEAK 34(XQ21.33) MUTATED                                                2
  DEL PEAK 34(XQ21.33) WILD-TYPE                                              8
                                vv
clus                             POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  DEL PEAK 34(XQ21.33) MUTATED                                                                                  11
  DEL PEAK 34(XQ21.33) WILD-TYPE                                                                                43
                                vv
clus                             PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  DEL PEAK 34(XQ21.33) MUTATED                                                                                             13
  DEL PEAK 34(XQ21.33) WILD-TYPE                                                                                           64
D57V29, multiclass
                                                                                              clus
vv                                                                                             DEL PEAK 34(XQ21.33) MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                           2
  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)                           13
                                                                                              clus
vv                                                                                             DEL PEAK 34(XQ21.33) 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)                                        43
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                             64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V30, binary
                                cls
clus                              0  1
  DEL PEAK 34(XQ21.33) MUTATED    9 12
  DEL PEAK 34(XQ21.33) WILD-TYPE 45 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(XQ21.33) MUTATED      9   12
  DEL PEAK 34(XQ21.33) WILD-TYPE   45   47
         clus
vv        DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  ABSENT                             9                             45
  PRESENT                           12                             47
[1] 2 2
[1] FALSE
D57V31, continuous
D57V32, continuous
D57V33, binary
                                cls
clus                              0  1
  DEL PEAK 34(XQ21.33) MUTATED   13 15
  DEL PEAK 34(XQ21.33) WILD-TYPE 22 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(XQ21.33) MUTATED     13   15
  DEL PEAK 34(XQ21.33) WILD-TYPE   22   66
                                          clus
vv                                         DEL PEAK 34(XQ21.33) MUTATED
  KERATINIZING SQUAMOUS CELL CARCINOMA                               13
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                           15
                                          clus
vv                                         DEL PEAK 34(XQ21.33) WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                                 22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                             66
[1] 2 2
[1] FALSE
D57V34, continuous
                                vv
clus                             OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  DEL PEAK 34(XQ21.33) MUTATED       1                   23                   0
  DEL PEAK 34(XQ21.33) WILD-TYPE     2                   90                   5
D57V35, multiclass
                      clus
vv                     DEL PEAK 34(XQ21.33) MUTATED
  OTHER                                           1
  RADICAL HYSTERECTOMY                           23
  SIMPLE HYSTERECTOMY                             0
                      clus
vv                     DEL PEAK 34(XQ21.33) WILD-TYPE
  OTHER                                             2
  RADICAL HYSTERECTOMY                             90
  SIMPLE HYSTERECTOMY                               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CURRENT USER FORMER USER NEVER USED
  DEL PEAK 34(XQ21.33) MUTATED              2           7         10
  DEL PEAK 34(XQ21.33) WILD-TYPE            6          33         30
D57V36, multiclass
              clus
vv             DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  CURRENT USER                            2                              6
  FORMER USER                             7                             33
  NEVER USED                             10                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V37, continuous
D57V38, binary
                                cls
clus                              0  1
  DEL PEAK 34(XQ21.33) MUTATED   16  1
  DEL PEAK 34(XQ21.33) WILD-TYPE 57 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(XQ21.33) MUTATED     16    1
  DEL PEAK 34(XQ21.33) WILD-TYPE   57   13
         clus
vv        DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  ABSENT                            16                             57
  PRESENT                            1                             13
[1] 2 2
[1] FALSE
D57V39, continuous
[1] "Remove cluster labels:"       "DEL PEAK 34(XQ21.33) MUTATED"
clus
  DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE 
                             2                              7 
                    TCGA-C5-A1BN                     TCGA-C5-A1MH 
"DEL PEAK 34(XQ21.33) WILD-TYPE" "DEL PEAK 34(XQ21.33) WILD-TYPE" 
                    TCGA-C5-A1MP                     TCGA-EK-A2RO 
"DEL PEAK 34(XQ21.33) WILD-TYPE" "DEL PEAK 34(XQ21.33) WILD-TYPE" 
                    TCGA-HM-A3JK                     TCGA-MU-A51Y 
"DEL PEAK 34(XQ21.33) WILD-TYPE" "DEL PEAK 34(XQ21.33) WILD-TYPE" 
                    TCGA-MU-A8JM 
"DEL PEAK 34(XQ21.33) WILD-TYPE" 
                                vv
clus                             T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B
  DEL PEAK 34(XQ21.33) MUTATED     1    0   4   10    7  1   1    0    2   2
  DEL PEAK 34(XQ21.33) WILD-TYPE   1    1  18   41   14  2   5    6    6  11
                                vv
clus                             T3B T4 TX
  DEL PEAK 34(XQ21.33) MUTATED     0  0  0
  DEL PEAK 34(XQ21.33) WILD-TYPE   2  1  7
D57V40, multiclass
      clus
vv     DEL PEAK 34(XQ21.33) MUTATED DEL PEAK 34(XQ21.33) WILD-TYPE
  T1A                             1                              1
  T1A1                            0                              1
  T1B                             4                             18
  T1B1                           10                             41
  T1B2                            7                             14
  T2                              1                              2
  T2A                             1                              5
  T2A1                            0                              6
  T2A2                            2                              6
  T2B                             2                             11
  T3B                             0                              2
  T4                              0                              1
  TX                              0                              7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V41, continuous
